Proposed Changes to the Enzyme List

An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.

Contents

*EC 1.1.1.348

Accepted name: (3R)-2'-hydroxyisoflavanone reductase

Reaction: a (4R)-4,2'-dihydroxyisoflavan + NADP⁺ = a (3R)-2'-hydroxyisoflavanone + NADPH + H⁺

For diagram of reaction click here

Glossary: (3R)-vestitone = (3R)-2',7-dihydroxy-4'-methoxyisoflavanone

Other name(s): vestitone reductase; pterocarpin synthase (incorrect); pterocarpan synthase (incorrect)

Systematic name: (3R)-2'-hydroxyisoflavanone:NADP⁺ 4-oxidoreductase

Comments: This plant enzyme participates in the biosynthesis of the pterocarpan phytoalexins medicarpin, maackiain, and several forms of glyceollin. The ezyme has a strict stereo specificity for the 3R-isoflavanones.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118477-70-6

References:

1. Bless, W. and Barz, W. Isolation of pterocarpan synthase, the terminal enzyme of pterocarpan phytoalexin biosynthesis in cell-suspension cultures of Cicer arietinum. FEBS Lett. 235 (1988) 47-50.

2. Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372-22378. [PMID: 8071365]

3. Guo, L., Dixon, R.A. and Paiva, N.L. The ‘pterocarpan synthase’ of alfalfa: association and co-induction of vestitone reductase and 7,2'-dihydroxy-4'-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 356 (1994) 221-225. [PMID: 7805842]

4. Guo, L. and Paiva, N.L. Molecular cloning and expression of alfalfa (Medicago sativa L.) vestitone reductase, the penultimate enzyme in medicarpin biosynthesis. Arch. Biochem. Biophys. 320 (1995) 353-360. [PMID: 7625843]

5. Shao, H., Dixon, R.A. and Wang, X. Crystal structure of vestitone reductase from alfalfa (Medicago sativa L.). J. Mol. Biol. 369 (2007) 265-276. [PMID: 17433362]

EC 1.1.1.412

Accepted name: 2-alkyl-3-oxoalkanoate reductase

Reaction: a (2R,3S)-2-alkyl-3-hydroxyalkanoate + NADP⁺ = an (R)-2-alkyl-3-oxoalkanoate + NADPH + H⁺

Other name(s): oleD (gene name)

Systematic name: (2R,3S)-2-alkyl-3-hydroxyalkanoate:NADP⁺ oxidoreductase

Comments: The enzyme, found in certain bacterial species, is part of a pathway for the production of olefins.

References:

1. Bonnett, S.A., Papireddy, K., Higgins, S., del Cardayre, S. and Reynolds, K.A. Functional characterization of an NADPH dependent 2-alkyl-3-ketoalkanoic acid reductase involved in olefin biosynthesis in Stenotrophomonas maltophilia. Biochemistry 50 (2011) 9633-9640. [PMID: 21958090]

EC 1.1.1.413

Accepted name: A-factor type γ-butyrolactone 1'-reductase (1S-forming)

Reaction: a (3R,4R)-3-[(1S)-1-hydroxyalkyl]-4-(hydroxymethyl)oxolan-2-one + NADP⁺ = a (3R,4R)-3-alkanoyl-4-(hydroxymethyl)oxolan-2-one + NADPH + H⁺

Glossary: a (3R,4R)-3-[(1S)-1-hydroxyalkyl]-4-(hydroxymethyl)oxolan-2-one = a VB type γ-butyrolactone
a (3R,4R)-3-alkanoyl-4-(hydroxymethyl)oxolan-2-one = an A-factor type γ-butyrolactone

Other name(s): barS1 (gene name)

Systematic name: (3R,4R)-3-[(1S)-1-hydroxyalkyl]-4-(hydroxymethyl)oxolan-2-one:NADP⁺ 1'-oxidoreductase

Comments: The enzyme, which is found in bacteria that produce virginiae-butanolide (VB) type γ-butyrolactone autoregulators, reduces its substrate stereospecifically, forming a hydroxyl group in the (S) configuration.

References:

1. Shikura, N., Yamamura, J. and Nihira, T. barS1, a gene for biosynthesis of a γ-butyrolactone autoregulator, a microbial signaling molecule eliciting antibiotic production in Streptomyces species. J. Bacteriol. 184 (2002) 5151-5157. [PMID: 12193632]

[EC 1.1.5.6 Transferred entry: formate dehydrogenase-N. Now EC 1.17.5.3, formate dehydrogenase-N (EC 1.1.5.6 created 2010, deleted 2017)]

[EC 1.1.99.33 Transferred entry: formate dehydrogenase (acceptor). Now EC 1.17.99.7, formate dehydrogenase (acceptor) (EC 1.1.99.33 created 2010, deleted 2017)]

EC 1.1.99.41

Accepted name: 3-hydroxy-1,2-didehydro-2,3-dihydrotabersonine reductase

Reaction: (1) (3R)-3-hydroxy-16-methoxy-2,3-dihydrotabersonine + acceptor = (3R)-3-hydroxy-16-methoxy-1,2-didehydro-2,3-dihydrotabersonine + reduced acceptor
(2) (3R)-3-hydroxy-2,3-dihydrotabersonine + acceptor = (3R)-3-hydroxy-1,2-didehydro-2,3-dihydrotabersonine + reduced acceptor

For diagram of reaction, click here

Other name(s): T3R; tabersonine 3-reductase

Systematic name: (3R)-3-hydroxy-16-methoxy-2,3-dihydrotabersonine:acceptor oxidoreductase

Comments: This enzyme is involved in the biosynthesis of vindoline and vindorosine in the plant Catharanthus roseus (Madagascar periwinkle). In vivo, it functions in the direction of reduction. It has no activity with 3-epoxylated compounds, which can form spontaneously from its unstable substrates.

References:

1. Qu, Y., Easson, M.L., Froese, J., Simionescu, R., Hudlicky, T. and De Luca, V. Completion of the seven-step pathway from tabersonine to the anticancer drug precursor vindoline and its assembly in yeast. Proc. Natl Acad. Sci. USA 112 (2015) 6224-6229. [PMID: 25918424]

[EC 1.2.1.2 Transferred entry: formate dehydrogenase. Now EC 1.17.1.9, formate dehydrogenase (EC 1.2.1.2 created 1961, deleted 2017)]

[EC 1.2.1.43 Transferred entry: formate dehydrogenase (NADP⁺). Now EC 1.17.1.10, formate dehydrogenase (NADP⁺) (EC 1.2.1.43 created 1978, deleted 2017)]

[EC 1.2.1.93 Transferred entry: formate dehydrogenase (NAD⁺, ferredoxin). Now EC 1.17.1.11, formate dehydrogenase (NAD⁺, ferredoxin) (EC 1.2.1.93 created 2015, deleted 2017)]

[EC 1.2.2.3 Transferred entry: formate dehydrogenase (cytochrome-c-553). Now EC 1.17.2.3, formate dehydrogenase (cytochrome-c-553) (EC 1.2.2.3 created 1981, deleted 2017)]

[EC 1.2.99.9 Transferred entry: formate dehydrogenase (coenzyme F₄₂₀). Now EC 1.17.98.3, formate dehydrogenase (coenzyme F₄₂₀) (EC 1.2.99.9 created 2014, deleted 2017)]

EC 1.5.5.3

Accepted name: hydroxyproline dehydrogenase

Reaction: trans-4-hydroxy-L-proline + a quinone = (3R,5S)-3-hydroxy-1-pyrroline-5-carboxylate + a quinol

Other name(s): HYPDH; OH-POX; hydroxyproline oxidase; PRODH₂ (gene name)

Systematic name: trans-4-hydroxy-L-proline:quinone oxidoreductase

Comments: A flavoprotein (FAD). The enzyme from human also has low activity with L-proline (cf. EC 1.5.5.2, proline dehydrogenase).

References:

1. Cooper, S.K., Pandhare, J., Donald, S.P. and Phang, J.M. A novel function for hydroxyproline oxidase in apoptosis through generation of reactive oxygen species. J. Biol. Chem. 283 (2008) 10485-10492. [PMID: 18287100]

2. Summitt, C.B., Johnson, L.C., Jonsson, T.J., Parsonage, D., Holmes, R.P. and Lowther, W.T. Proline dehydrogenase 2 (PRODH₂) is a hydroxyproline dehydrogenase (HYPDH) and molecular target for treating primary hyperoxaluria. Biochem. J. 466 (2015) 273-281. [PMID: 25697095]

EC 1.5.98.3

Accepted name: coenzyme F₄₂₀:methanophenazine dehydrogenase

Reaction: reduced coenzyme F₄₂₀ + methanophenazine = oxidized coenzyme F₄₂₀ + dihydromethanophenazine

Glossary: methanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}phenazine
dihydromethanophenazine = 2-{[(6E,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl]oxy}-5,10-dihydrophenazine

Other name(s): F₄₂₀H₂ dehydrogenase; fpoBCDIF (gene names)

Systematic name: reduced coenzyme F₄₂₀:methanophenazine oxidoreductase

Comments: The enzyme, found in some methanogenic archaea, is responsible for the reoxidation of coenzyme F₄₂₀, which is reduced during methanogenesis, and for the reduction of methanophenazine to dihydromethanophenazine, which is required by EC 1.8.98.1, dihydromethanophenazine:CoB-CoM heterodisulfide reductase. The enzyme is membrane-bound, and is coupled to proton translocation across the cytoplasmic membrane, generating a proton motive force that is used for ATP generation.

References:

1. Brodersen, J., Gottschalk, G. and Deppenmeier, U. Membrane-bound F₄₂₀H₂-dependent heterodisulfide reduction in Methanococcus volta. Arch. Microbiol. 171 (1999) 115-121. [PMID: 9914308]

2. Baumer, S., Ide, T., Jacobi, C., Johann, A., Gottschalk, G. and Deppenmeier, U. The F₄₂₀H₂ dehydrogenase from Methanosarcina mazei is a Redox-driven proton pump closely related to NADH dehydrogenases. J. Biol. Chem. 275 (2000) 17968-17973. [PMID: 10751389]

3. Deppenmeier, U. The membrane-bound electron transport system of Methanosarcina species. J. Bioenerg. Biomembr. 36 (2004) 55-64. [PMID: 15168610]

4. Abken H. J. and Deppenmeier, U. Purification and properties of an F₄₂₀H₂ dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (2006) 231-237.

EC 1.8.1.20

Accepted name: 4,4'-dithiodibutanoate disulfide reductase

Reaction: 2 4-sulfanylbutanoate + NAD⁺ = 4,4'-disulfanediyldibutanoate + NADH + H⁺

Systematic name: 4-sulfanylbutanoate:NAD⁺ oxidoreductase

Comments: The enzyme, characterized from the bacterium Rhodococcus erythropolis MI2, contains an FMN cofator.

References:

1. Khairy, H., Wubbeler, J.H. and Steinbuchel, A. Biodegradation of the organic disulfide 4,4'-dithiodibutyric acid by Rhodococcus spp. Appl. Environ. Microbiol. 81 (2015) 8294-8306. [PMID: 26407888]

2. Khairy, H., Wubbeler, J.H. and Steinbuchel, A. The NADH:flavin oxidoreductase Nox from Rhodococcus erythropolis MI2 is the key enzyme of 4,4'-dithiodibutyric acid degradation. Lett. Appl. Microbiol. 63 (2016) 434-441. [PMID: 27564089]

EC 1.8.3.7

Accepted name: formylglycine-generating enzyme

Reaction: a [sulfatase]-L-cysteine + O₂ + 2 a thiol = a [sulfatase]-3-oxo-L-alanine + hydrogen sulfide + a disulfide + H₂O

Glossary: 3-oxo-L-alanine = formylglycine = Cα-formylglycine = FGly

Other name(s): sulfatase-modifying factor 1; Cα-formylglycine-generating enzyme 1; SUMF1 (gene name)

Systematic name: [sulfatase]-L-cysteine:oxygen oxidoreductase (3-oxo-L-alanine-forming)

Comments: Requires a copper cofactor and Ca²⁺. The enzyme, which is found in both prokaryotes and eukaryotes, catalyses a modification of a conserved L-cysteine residue in the active site of sulfatases, generating a unique 3-oxo-L-alanine residue that is essential for sulfatase activity. The exact nature of the thiol involved is still not clear - dithiothreitol and cysteamine are the most efficiently used thiols in vitro. Glutathione alo acts in vitro, but it is not known whether it is used in vivo.

References:

1. Dierks, T., Schmidt, B. and von Figura, K. Conversion of cysteine to formylglycine: a protein modification in the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 94 (1997) 11963-11968. [PMID: 9342345]

2. Dierks, T., Miech, C., Hummerjohann, J., Schmidt, B., Kertesz, M.A. and von Figura, K. Posttranslational formation of formylglycine in prokaryotic sulfatases by modification of either cysteine or serine. J. Biol. Chem. 273 (1998) 25560-25564. [PMID: 9748219]

3. Preusser-Kunze, A., Mariappan, M., Schmidt, B., Gande, S.L., Mutenda, K., Wenzel, D., von Figura, K. and Dierks, T. Molecular characterization of the human Cα-formylglycine-generating enzyme. J. Biol. Chem. 280 (2005) 14900-14910. [PMID: 15657036]

4. Roeser, D., Preusser-Kunze, A., Schmidt, B., Gasow, K., Wittmann, J.G., Dierks, T., von Figura, K. and Rudolph, M.G. A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme. Proc. Natl. Acad. Sci. USA 103 (2006) 81-86. [PMID: 16368756]

5. Carlson, B.L., Ballister, E.R., Skordalakes, E., King, D.S., Breidenbach, M.A., Gilmore, S.A., Berger, J.M. and Bertozzi, C.R. Function and structure of a prokaryotic formylglycine-generating enzyme. J. Biol. Chem. 283 (2008) 20117-20125. [PMID: 18390551]

6. Holder, P.G., Jones, L.C., Drake, P.M., Barfield, R.M., Banas, S., de Hart, G.W., Baker, J. and Rabuka, D. Reconstitution of formylglycine-generating enzyme with copper(II) for aldehyde tag conversion. J. Biol. Chem. 290 (2015) 15730-15745. [PMID: 25931126]

7. Knop, M., Engi, P., Lemnaru, R. and Seebeck, F.P. In vitro reconstitution of formylglycine-generating enzymes requires copper(I). Chembiochem 16 (2015) 2147-2150. [PMID: 26403223]

8. Knop, M., Dang, T.Q., Jeschke, G. and Seebeck, F.P. Copper is a cofactor of the formylglycine-generating enzyme. Chembiochem 18 (2017) 161-165. [PMID: 27862795]

9. Meury, M., Knop, M. and Seebeck, F.P. Structural basis for copper-oxygen mediated C-H bond activation by the formylglycine-generating enzyme. Angew. Chem. Int. Ed. Engl. (2017) . [PMID: 28544744]

*EC 1.10.3.14

Accepted name: ubiquinol oxidase (electrogenic, non H⁺-transporting)

Reaction: 2 ubiquinol + O_{2[side 2]} + 4 H⁺_{[side 2]} = 2 ubiquinone + 2 H₂O_{[side 2]} + 4 H⁺_{[side 1]} (overall reaction)
(1a) 2 ubiquinol = 2 ubiquinone + 4 H⁺_{[side 1]} + 4 e^-
(1b) O_{2[side 2]} + 4 H⁺_{[side 2]} + 4 e^- = 2 H₂O_{[side 2]}

Other name(s): cytochrome bd-I oxidase; cydA (gene name); cydB (gene name); ubiquinol:O₂ oxidoreductase (electrogenic, non H⁺-transporting)

Systematic name: ubiquinol:oxygen oxidoreductase (electrogenic, non H⁺-transporting)

Comments: This terminal oxidase enzyme is unable to pump protons but generates a proton motive force by transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) is 1. The bd-I oxidase from the bacterium Escherichia coli is the predominant respiratory oxygen reductase that functions under microaerophilic conditions in that organism. cf. EC 1.10.3.10, ubiquinol oxidase (H⁺-transporting).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Miller, M.J., Hermodson, M. and Gennis, R.B. The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits. J. Biol. Chem. 263 (1988) 5235-5240. [PMID: 3281937]

2. Puustinen, A., Finel, M., Haltia, T., Gennis, R.B. and Wikstrom, M. Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30 (1991) 3936-3942. [PMID: 1850294]

3. Belevich, I., Borisov, V.B., Zhang, J., Yang, K., Konstantinov, A.A., Gennis, R.B. and Verkhovsky, M.I. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc. Natl. Acad. Sci. USA 102 (2005) 3657-3662. [PMID: 15728392]

4. Lenn, T., Leake, M.C. and Mullineaux, C.W. Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo. Mol. Microbiol. 70 (2008) 1397-1407. [PMID: 19019148]

EC 1.13.11.83

Accepted name: 4-hydroxy-3-prenylphenylpyruvate oxygenase

Reaction: 3-dimethylallyl-4-hydroxyphenylpyruvate + O₂ = 3-dimethylallyl-4-hydroxymandelate + CO₂

For diagram of reaction, click here

Other name(s): CloR

Systematic name: 3-dimethylallyl-4-hydroxyphenylpyruvate:oxygen 1,2-oxidoreductase (3-dimethylallyl-4-hydroxymandelate forming)

Comments: Requires non-heme-Fe(II). Isolated from the bacterium Streptomyces roseochromogenes DS 12976. A bifunctional enzyme involved in clorobiocin biosynthesis that also catalyses the activity of EC 1.13.12.23, 3-dimethylallyl-4-hydroxybenzoate synthase.

References:

1. Pojer, F., Kahlich, R., Kammerer, B., Li, S.M. and Heide, L. CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis. J. Biol. Chem. 278 (2003) 30661-30668. [PMID: 12777382]

*EC 1.13.12.5

Accepted name: Renilla-type luciferase

Reaction: coelenterazine h + O₂ = excited coelenteramide h monoanion + CO₂ (over-all reaction)
(1a) coelenterazine h + O₂ = coelenterazine h dioxetanone
(1b) coelenterazine h dioxetanone = excited coelenteramide h monoanion + CO₂

For diagram of reaction, click here

Glossary: coelenterazine h = Renilla luciferin = 2,8-dibenzyl-6-(4-hydroxyphenyl)imidazo[1,2-a]pyrazin-3(7H)-one
coelenteramide h = Renilla oxyluciferin = N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-phenylacetamide

Other name(s): Renilla-luciferin 2-monooxygenase; luciferase (Renilla luciferin); Renilla-luciferin:oxygen 2-oxidoreductase (decarboxylating)

Systematic name: coelenterazine h:oxygen 2-oxidoreductase (decarboxylating)

Comments: This enzyme has been studied from the soft coral Renilla reniformis. Before the reaction occurs the substrate is sequestered by a coelenterazine-binding protein. Elevation in the concentration of calcium ions releases the substrate, which then interacts with the luciferase. Upon binding the substrate, the enzyme catalyses an oxygenation, producing a very short-lived hydroperoxide that cyclizes into a dioxetanone structure, which collapses, releasing a CO₂ molecule. The spontaneous breakdown of the dioxetanone releases the energy (about 50 kcal/mole) that is necessary to generate the excited state of the coelenteramide product, which is the singlet form of the monoanion. In vivo the product undergoes the process of nonradiative energy transfer to an accessory protein, a green fluorescent protein (GFP), which results in green bioluminescence. In vitro, in the absence of GFP, the product emits blue light.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61869-41-8

References:

1. Cormier, M.J., Hori, K. and Anderson, J.M. Bioluminescence in coelenterates. Biochim. Biophys. Acta 346 (1974) 137-164. [PMID: 4154104]

2. Hori, K., Anderson, J.M., Ward, W.W. and Cormier, M.J. Renilla luciferin as the substrate for calcium induced photoprotein bioluminescence. Assignment of luciferin tautomers in aequorin and mnemiopsin. Biochemistry 14 (1975) 2371-2376. [PMID: 237531]

3. Anderson, J.M., Charbonneau, H. and Cormier, M.J. Mechanism of calcium induction of Renilla bioluminescence. Involvement of a calcium-triggered luciferin binding protein. Biochemistry 13 (1974) 1195-1200. [PMID: 4149963]

4. Shimomura, O. and Johnson, F.H. Chemical nature of bioluminescence systems in coelenterates. Proc. Natl. Acad. Sci. USA 72 (1975) 1546-1549. [PMID: 236561]

5. Charbonneau, H. and Cormier, M.J. Ca²⁺-induced bioluminescence in Renilla reniformis. Purification and characterization of a calcium-triggered luciferin-binding protein. J. Biol. Chem. 254 (1979) 769-780. [PMID: 33174]

6. Lorenz, W.W., McCann, R.O., Longiaru, M. and Cormier, M.J. Isolation and expression of a cDNA encoding Renilla reniformis luciferase. Proc. Natl. Acad. Sci. USA 88 (1991) 4438-4442. [PMID: 1674607]

7. Loening, A.M., Fenn, T.D. and Gambhir, S.S. Crystal structures of the luciferase and green fluorescent protein from Renilla reniformis. J. Mol. Biol. 374 (2007) 1017-1028. [PMID: 17980388]

EC 1.13.12.23

Accepted name: 4-hydroxy-3-prenylbenzoate synthase

Reaction: 3-dimethylallyl-4-hydroxymandelate + O₂ = 3-dimethylallyl-4-hydroxybenzoate + CO₂ + H₂O

For diagram of reaction, click here

Other name(s): CloR; novR (gene name)

Systematic name: 3-dimethylallyl-4-hydroxymandelate:oxygen oxidoreductase (3-dimethylallyl-4-hydroxybenzoate forming)

Comments: Isolated from the bacterium Streptomyces roseochromogenes DS 12976. A bifunctional enzyme involved in clorobiocin biosynthesis that also catalyses the activity of EC 1.13.11.83, 3-dimethylallyl-4-hydroxyphenylpyruvate oxygenase.

References:

1. Pojer, F., Kahlich, R., Kammerer, B., Li, S.M. and Heide, L. CloR, a bifunctional non-heme iron oxygenase involved in clorobiocin biosynthesis. J. Biol. Chem. 278 (2003) 30661-30668. [PMID: 12777382]

*EC 1.14.11.2

Accepted name: procollagen-proline 4-dioxygenase

Reaction: procollagen L-proline + 2-oxoglutarate + O₂ = procollagen trans-4-hydroxy-L-proline + succinate + CO₂

For diagram of reaction, click here

Other name(s): P4HA (gene name); P4HB (gene name); protocollagen hydroxylase; proline hydroxylase; proline,2-oxoglutarate 4-dioxygenase; collagen proline hydroxylase; hydroxylase, collagen proline; peptidyl proline hydroxylase; proline protocollagen hydroxylase; proline, 2-oxoglutarate dioxygenase; prolyl hydroxylase; prolylprotocollagen dioxygenase; prolylprotocollagen hydroxylase; protocollagen proline 4-hydroxylase; protocollagen proline dioxygenase; protocollagen proline hydroxylase; protocollagen prolyl hydroxylase; prolyl 4-hydroxylase; prolyl-glycyl-peptide, 2-oxoglutarate:oxygen oxidoreductase, 4-hydroxylating; procollagen-proline 4-dioxygenase (ambiguous)

Systematic name: procollagen-L-proline,2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)

Comments: Requires Fe²⁺ and ascorbate.The enzyme, which is located within the lumen of the endoplasmic reticulum, catalyses the 4-hydroxylation of prolines in -X-Pro-Gly- sequences. The 4-hydroxyproline residues are essential for the formation of the collagen triple helix. The enzyme forms a complex with protein disulfide isomerase and acts not only on procollagen but also on more than 15 other proteins that have collagen-like domains.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-06-2

References:

1. Hutton, J.J., Jr., Tappel, A.L. and Udenfriend, S. Cofactor and substrate requirements of collagen proline hydroxylase. Arch. Biochem. Biophys. 118 (1967) 231-240.

2. Kivirikko, K.I. and Prockop, D.J. Purification and partial characterization of the enzyme for the hydroxylation of proline in protocollogen. Arch. Biochem. Biophys. 118 (1967) 611-618.

3. Kivirikko, K.I., Kishida, Y., Sakakibara, S. and Prockop, J. Hydroxylation of (X-Pro-Gly)n by protocollagen proline hydroxylase. Effect of chain length, helical conformation and amino acid sequence in the substrate. Biochim. Biophys. Acta 271 (1972) 347-356. [PMID: 5046811]

4. Berg, R.A. and Prockop, D.J. Affinity column purification of protocollagen proline hydroxylase from chick embryos and further characterization of the enzyme. J. Biol. Chem. 248 (1973) 1175-1182. [PMID: 4346946]

5. John, D.C. and Bulleid, N.J. Prolyl 4-hydroxylase: defective assembly of α-subunit mutants indicates that assembled α-subunits are intramolecularly disulfide bonded. Biochemistry 33 (1994) 14018-14025. [PMID: 7947811]

6. Lamberg, A., Pihlajaniemi, T. and Kivirikko, K.I. Site-directed mutagenesis of the α subunit of human prolyl 4-hydroxylase. Identification of three histidine residues critical for catalytic activity. J. Biol. Chem. 270 (1995) 9926-9931. [PMID: 7730375]

7. Myllyharju, J. and Kivirikko, K.I. Characterization of the iron- and 2-oxoglutarate-binding sites of human prolyl 4-hydroxylase. EMBO J. 16 (1997) 1173-1180. [PMID: 9135134]

8. Kivirikko, K.I. and Myllyharju, J. Prolyl 4-hydroxylases and their protein disulfide isomerase subunit. Matrix Biol 16 (1998) 357-368. [PMID: 9524356]

[EC 1.14.13.48 Transferred entry: (S)-limonene 6-monooxygenase. Now classified as EC 1.14.14.51, (S)-limonene 6-monooxygenase (EC 1.14.13.48 created 1992, modified 2003, deleted 2017)]

[EC 1.14.13.49 Transferred entry: (S)-limonene 7-monooxygenase. Now classified as EC 1.14.14.52, (S)-limonene 7-monooxygenase (EC 1.14.13.49 created 1992, modified 2003, deleted 2017)]

[EC 1.14.13.72 Transferred entry: methylsterol monooxygenase. Now classified as EC 1.14.18.9, methylsterol monooxygenase (EC 1.14.13.72 created 1972 as EC 1.14.99.16, transferred 2002 to EC 1.14.13.72, deleted 2017)]

[EC 1.14.13.80 Transferred entry: (R)-limonene 6-monooxygenase. Now classified as EC 1.14.14.53, (R)-limonene 6-monooxygenase (EC 1.14.13.80 created 2003, deleted 2017)]

EC 1.14.13.237

Accepted name: aliphatic glucosinolate S-oxygenase

Reaction: an ω-(methylthio)alkyl-glucosinolate + NADPH + H⁺ + O₂ = an ω-(methylsulfinyl)alkyl-glucosinolate + NADP⁺ + H₂O

Glossary: ω-(methylthio)alkyl-glucosinolate = an ω-(methylthio)-N-sulfo-alkylhydroximate S-glucoside

Other name(s): ω-(methylthio)alkylglucosinolate S-oxygenase; GS-OX1 (gene name)

Systematic name: ω-(methylthio)alkyl-glucosinolate,NADPH:oxygen S-oxidoreductase

Comments: The enzyme is a member of the flavin-dependent monooxygenase (FMO) family (cf. EC 1.14.13.8). The plant Arabidopsis thaliana contains five isoforms. GS-OX1 through GS-OX4 are able to catalyse the S-oxygenation independent of chain length, while GS-OX5 is specific for 8-(methylthio)octyl glucosinolate.

References:

1. Hansen, B.G., Kliebenstein, D.J. and Halkier, B.A. Identification of a flavin-monooxygenase as the S-oxygenating enzyme in aliphatic glucosinolate biosynthesis in Arabidopsis. Plant J. 50 (2007) 902-910. [PMID: 17461789]

2. Li, J., Hansen, B.G., Ober, J.A., Kliebenstein, D.J. and Halkier, B.A. Subclade of flavin-monooxygenases involved in aliphatic glucosinolate biosynthesis. Plant Physiol. 148 (2008) 1721-1733. [PMID: 18799661]

EC 1.14.13.238

Accepted name: dimethylamine monooxygenase

Reaction: dimethylamine + NADPH + H⁺ + O₂ = methylamine + formaldehyde + NADP⁺ + H₂O

Other name(s): dmmABC (gene names)

Systematic name: dimethylamine,NADPH:oxygen oxidoreductase (formaldehyde-forming)

Comments: The enzyme, characterized from several bacterial species, is involved in a pathway for the degradation of methylated amines. It is composed of three subunits, one of which is a ferredoxin, and contains heme iron and an FMN cofactor.

References:

1. Eady, R.R. and Large, P.J. Bacterial oxidation of dimethylamine, a new mono-oxygenase reaction. Biochem. J. 111 (1969) 37P-38P. [PMID: 4389011]

2. Eady, R.R., Jarman, T.R. and Large, P.J. Microbial oxidation of amines. Partial purification of a mixed-function secondary-amine oxidase system from Pseudomonas aminovorans that contains an enzymically active cytochrome-P-420-type haemoprotein. Biochem. J. 125 (1971) 449-459. [PMID: 4401380]

3. Alberta, J.A. and Dawson, J.H. Purification to homogeneity and initial physical characterization of secondary amine monooxygenase. J. Biol. Chem. 262 (1987) 11857-11863. [PMID: 3624236]

4. Lidbury, I., Mausz, M.A., Scanlan, D.J. and Chen, Y. Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway. LID - 10.1038/ismej.2017.31 [doi. ISME J. (2017) . [PMID: 28304370]

EC 1.14.14.48

Accepted name: jasmonoyl-L-amino acid 12-hydroxylase

Reaction: a jasmonoyl-L-amino acid + [reduced NADPH —hemoprotein reductase] + O₂ = a 12-hydroxyjasmonoyl-L-amino acid + [oxidized NADPH —hemoprotein reductase] + H₂O

Glossary: jasmonic acid = {(1R,2R)-3-oxo-2-[(2Z)pent-2-en-1-yl]cyclopentyl}acetic acid
(+)-7-epi-jasmonic acid = {(1R,2S)-3-oxo-2-[(2Z)pent-2-en-1-yl]cyclopentyl}acetic acid

Other name(s): CYP94B1 (gene name); CYP94B3 (gene name)

Systematic name: jasmonoyl-L-amino acid,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (12-hydroxylating)

Comments: A cytochrome P450 (heme thiolate) enzyme found in plants. The enzyme acts on jasmonoyl-L-amino acid conjugates, catalysing the hydroxylation of the C-12 position of jasmonic acid. While the best studied substrate is (+)-7-epi-jasmonoyl-L-isoleucine, the enzyme was shown to be active with jasmonoyl-L-valine and jasmonoyl-L-phenylalanine, and is likely to be active with other jasmonoyl-amino acid conjugates.

References:

1. Koo, A.J., Cooke, T.F. and Howe, G.A. Cytochrome P450 CYP94B3 mediates catabolism and inactivation of the plant hormone jasmonoyl-L-isoleucine. Proc. Natl. Acad. Sci. USA 108 (2011) 9298-9303. [PMID: 21576464]

2. Kitaoka, N., Matsubara, T., Sato, M., Takahashi, K., Wakuta, S., Kawaide, H., Matsui, H., Nabeta, K. and Matsuura, H. Arabidopsis CYP94B3 encodes jasmonyl-L-isoleucine 12-hydroxylase, a key enzyme in the oxidative catabolism of jasmonate. Plant Cell Physiol 52 (2011) 1757-1765. [PMID: 21849397]

3. Heitz, T., Widemann, E., Lugan, R., Miesch, L., Ullmann, P., Desaubry, L., Holder, E., Grausem, B., Kandel, S., Miesch, M., Werck-Reichhart, D. and Pinot, F. Cytochromes P450 CYP94C1 and CYP94B3 catalyze two successive oxidation steps of plant hormone jasmonoyl-isoleucine for catabolic turnover. J. Biol. Chem. 287 (2012) 6296-6306. [PMID: 22215670]

4. Kitaoka, N., Kawaide, H., Amano, N., Matsubara, T., Nabeta, K., Takahashi, K. and Matsuura, H. CYP94B3 activity against jasmonic acid amino acid conjugates and the elucidation of 12-O-β-glucopyranosyl-jasmonoyl-L-isoleucine as an additional metabolite. Phytochemistry 99 (2014) 6-13. [PMID: 24467969]

5. Koo, A.J., Thireault, C., Zemelis, S., Poudel, A.N., Zhang, T., Kitaoka, N., Brandizzi, F., Matsuura, H. and Howe, G.A. Endoplasmic reticulum-associated inactivation of the hormone jasmonoyl-L-isoleucine by multiple members of the cytochrome P450 94 family in Arabidopsis. J. Biol. Chem. 289 (2014) 29728-29738. [PMID: 25210037]

6. Widemann, E., Grausem, B., Renault, H., Pineau, E., Heinrich, C., Lugan, R., Ullmann, P., Miesch, L., Aubert, Y., Miesch, M., Heitz, T. and Pinot, F. Sequential oxidation of jasmonoyl-phenylalanine and jasmonoyl-isoleucine by multiple cytochrome P450 of the CYP94 family through newly identified aldehyde intermediates. Phytochemistry 117 (2015) 388-399. [PMID: 26164240]

EC 1.14.14.49

Accepted name: 12-hydroxyjasmonoyl-L-amino acid 12-hydroxylase

Reaction: a 12-hydroxyjasmonoyl-L-amino acid + 2 [reduced NADPH —hemoprotein reductase] + 2 O₂ = a 12-hydroxy-12-oxojasmonoyl-L-amino acid + 2 [oxidized NADPH —hemoprotein reductase] + 3 H₂O (overall reaction)
(1a) a 12-hydroxyjasmonoyl-L-amino acid + [reduced NADPH —hemoprotein reductase] + O₂ = a 12-oxojasmonoyl-L-amino acid + [oxidized NADPH —hemoprotein reductase] + 2 H₂O
(1b) a 12-oxojasmonoyl-L-amino acid + [reduced NADPH —hemoprotein reductase] + O₂ = a 12-hydroxy-12-oxojasmonoyl-L-amino acid + [oxidized NADPH —hemoprotein reductase] + H₂O

Glossary: (3Z)-5-[(1R,2R)-2-(carboxymethyl)-5-oxocyclopentyl]pent-3-enoate = 12-hydroxy-12-oxojasmonate

Other name(s): CYP94C1 (gene name)

Systematic name: 12-hydroxyjasmonoyl-L-amino acid,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (12-hydroxylating)

Comments: A cytochrome P450 (heme thiolate) enzyme found in plants. The enzyme acts on jasmonoyl-L-amino acid conjugates that have been hydroxylated at the C-12 position of jasmonic acid by EC 1.14.14.48, jasmonoyl-L-amino acid 12-hydroxylase, further oxidizing that position to a carboxylate via an aldehyde intermediate. While the best studied substrate is (+)-7-epi-jasmonoyl-L-isoleucine, the enzyme was shown to be active with jasmonoyl-L-phenylalanine, and is likely to be active with other jasmonoyl-amino acid conjugates.

References:

1. Heitz, T., Widemann, E., Lugan, R., Miesch, L., Ullmann, P., Desaubry, L., Holder, E., Grausem, B., Kandel, S., Miesch, M., Werck-Reichhart, D. and Pinot, F. Cytochromes P450 CYP94C1 and CYP94B3 catalyze two successive oxidation steps of plant hormone jasmonoyl-isoleucine for catabolic turnover. J. Biol. Chem. 287 (2012) 6296-6306. [PMID: 22215670]

2. Widemann, E., Grausem, B., Renault, H., Pineau, E., Heinrich, C., Lugan, R., Ullmann, P., Miesch, L., Aubert, Y., Miesch, M., Heitz, T. and Pinot, F. Sequential oxidation of jasmonoyl-phenylalanine and jasmonoyl-isoleucine by multiple cytochrome P450 of the CYP94 family through newly identified aldehyde intermediates. Phytochemistry 117 (2015) 388-399. [PMID: 26164240]

3. Bruckhoff, V., Haroth, S., Feussner, K., Konig, S., Brodhun, F. and Feussner, I. Functional characterization of CYP94-genes and identification of a novel jasmonate catabolite in flowers. PLoS One 11 (2016) e0159875. [PMID: 27459369]

EC 1.14.14.50

Accepted name: tabersonine 3-oxygenase

Reaction: (1) 16-methoxytabersonine + [reduced NADPH —hemoprotein reductase] + O₂ = (3R)-3-hydroxy-16-methoxy-1,2-didehydro-2,3-dihydrotabersonine + [oxidized NADPH —hemoprotein reductase] + H₂O
(2) tabersonine + [reduced NADPH —hemoprotein reductase] + O₂ = (3R)-3-hydroxy-1,2-didehydro-2,3-dihydrotabersonine + [oxidized NADPH —hemoprotein reductase] + H₂O

For diagram of reaction, click here

Other name(s): T3O; CYP71D1V2

Systematic name: 16-methoxytabersonine,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (3-hydroxylating)

Comments: This cytochrome P-450 (heme thiolate) enzyme acts on 16-methoxytabersonine, leading to biosynthesis of vindoline in the plant Catharanthus roseus (Madagascar periwinkle). It can also act on tabersonine, resulting in the production of small amounts of vindorosine. The products are unstable and, in the absence of EC 1.1.99.41, 3-hydroxy-1,2-didehydro-2,3-dihydrotabersonine reductase, will convert into 3-epoxylated compounds.

References:

1. Qu, Y., Easson, M.L., Froese, J., Simionescu, R., Hudlicky, T. and De Luca, V. Completion of the seven-step pathway from tabersonine to the anticancer drug precursor vindoline and its assembly in yeast. Proc. Natl Acad. Sci. USA 112 (2015) 6224-6229. [PMID: 25918424]

EC 1.14.14.51

Accepted name: (S)-limonene 6-monooxygenase

Reaction: (S)-limonene + [reduced NADPH —hemoprotein reductase] + O₂ = (–)-trans-carveol + [oxidized NADPH —hemoprotein reductase] + H₂O

For diagram of reaction click here

Glossary: limonene = a monoterpenoid
(S)-limonene = (–)-limonene

Other name(s): (–)-limonene 6-hydroxylase; (–)-limonene 6-monooxygenase; (–)-limonene,NADPH:oxygen oxidoreductase (6-hydroxylating)

Systematic name: (S)-limonene,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (6-hydroxylating)

Comments: A cytochrome P-450 (heme thiolate) enzyme. The enzyme participates in the biosynthesis of (–)-carvone, which is responsible for the aroma of spearmint.

References:

1. Karp, F., Mihaliak, C.A., Harris, J.L. and Croteau, R. Monoterpene biosynthesis: specificity of the hydroxylations of (–)-limonene by enzyme preparations from peppermint (Mentha piperita), spearmint (Mentha spicata), and perilla (Perilla frutescens) leaves. Arch. Biochem. Biophys. 276 (1990) 219-226. [PMID: 2297225]

EC 1.14.14.52 Accepted name: (S)-limonene 7-monooxygenase

Reaction: (S)-limonene + [reduced NADPH —hemoprotein reductase] + O₂ = (–)-perillyl alcohol + [oxidized NADPH —hemoprotein reductase] + H₂O

For diagram of reaction click here

Glossary: limonene = a monoterpenoid
(S)-limonene = (–)-limonene

Other name(s): (–)-limonene 7-monooxygenase; (–)-limonene hydroxylase; (–)-limonene monooxygenase; (–)-limonene,NADPH:oxygen oxidoreductase (7-hydroxylating)

Systematic name: (S)-limonene,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (7-hydroxylating)

Comments: A cytochrome P-450 (heme thiolate) enzyme. The enzyme, characterized from the plant Perilla frutescens, participates in the biosynthesis of perillyl aldehyde, the major constituent of the essential oil that accumulates in the glandular trichomes of this plant. Some forms of the enzyme also catalyse the oxidation of (–)-perillyl alcohol to (–)-perillyl aldehyde.

References:

1. Karp, F., Mihaliak, C.A., Harris, J.L. and Croteau, R. Monoterpene biosynthesis: specificity of the hydroxylations of (–)-limonene by enzyme preparations from peppermint (Mentha piperita), spearmint (Mentha spicata), and perilla (Perilla frutescens) leaves. Arch. Biochem. Biophys. 276 (1990) 219-226. [PMID: 2297225]

2. Mau, C.J., Karp, F., Ito, M., Honda, G. and Croteau, R.B. A candidate cDNA clone for (–)-limonene-7-hydroxylase from Perilla frutescens. Phytochemistry 71 (2010) 373-379. [PMID: 20079506]

3. Fujiwara, Y. and Ito, M. Molecular cloning and characterization of a Perilla frutescens cytochrome P450 enzyme that catalyzes the later steps of perillaldehyde biosynthesis. Phytochemistry 134 (2017) 26-37. [PMID: 27890582]

EC 1.14.14.53

Accepted name: (R)-limonene 6-monooxygenase

Reaction: (R)-limonene + [reduced NADPH —hemoprotein reductase] + O₂ = (+)-trans-carveol + [oxidized NADPH —hemoprotein reductase] + H₂O

For diagram of reaction click here

Glossary: limonene = a monoterpenoid
(R)-limonene = (+)-limonene

Other name(s): (+)-limonene-6-hydroxylase; (+)-limonene 6-monooxygenase

Systematic name: (R)-limonene,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (6-hydroxylating)

Comments: The reaction is stereospecific with over 95% yield of (+)-trans-carveol from (R)-limonene. (S)-Limonene, the substrate for EC 1.14.14.51, (S)-limonene 6-monooxygenase, is not a substrate. Forms part of the carvone biosynthesis pathway in Carum carvi (caraway) seeds.

References:

1. Bouwmeester, H.J., Gershenzon, J., Konings, M.C.J.M. and Croteau, R. Biosynthesis of the monoterpenes limonene and carvone in the fruit of caraway. I. Demonstration of enzyme activities and their changes with development. Plant Physiol. 117 (1998) 901-912. [PMID: 9662532]

2. Bouwmeester, H.J., Konings, M.C.J.M., Gershenzon, J., Karp, F. and Croteau, R. Cytochrome P-450 dependent (+)-limonene-6-hydroxylation in fruits of caraway (Carum carvi). Phytochemistry 50 (1999) 243-248.

EC 1.14.14.54

Accepted name: phenylacetate 2-hydroxylase

Reaction: phenylacetate + [reduced NADPH —hemoprotein reductase] + O₂ = (2-hydroxyphenyl)acetate + [oxidized NADPH —hemoprotein reductase] + H₂O

Other name(s): CYP504; phaA (gene name)

Systematic name: phenylacetate,[reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (2-hydroxylating)

Comments: This cytochrome P-450 (heme-thiolate) enzyme, found in Aspergillus nidulans, is involved in the degradation of phenylacetate.

References:

1. Mingot, J.M., Penalva, M.A. and Fernandez-Canon, J.M. Disruption of phacA, an Aspergillus nidulans gene encoding a novel cytochrome P450 monooxygenase catalyzing phenylacetate 2-hydroxylation, results in penicillin overproduction. J. Biol. Chem. 274 (1999) 14545-14550. [PMID: 10329644]

2. Rodriguez-Saiz, M., Barredo, J.L., Moreno, M.A., Fernandez-Canon, J.M., Penalva, M.A. and Diez, B. Reduced function of a phenylacetate-oxidizing cytochrome P450 caused strong genetic improvement in early phylogeny of penicillin-producing strains. J. Bacteriol. 183 (2001) 5465-5471. [PMID: 11544206]

EC 1.14.15.23

Accepted name: chloroacetanilide N-alkylformylase

Reaction: butachlor + 2 reduced ferredoxin [iron-sulfur] cluster + O₂ = 2-chloro-N-(2,6-diethylphenyl)acetamide + butyl formate + 2 reduced ferredoxin [iron-sulfur] cluster + H₂O

Glossary: butachlor = N-(butoxymethyl)-2-chloro-N-(2,6-diethylphenyl)acetamide
acetochlor = N-(ethoxymethyl)-2-chloro-N-(2-ethyl,6-methylphenyl)acetamide
alachlor = N-(methoxymethyl)-2-chloro-N-(2,6-diethylphenyl)acetamide

Other name(s): cndA (gene name)

Systematic name: butachlor,ferredoxin:oxygen oxidoreductase (butyl formate-releasing)

Comments: The enzyme, characterized from the bacterium Sphingomonas sp. DC-6, initiates the degradation of several chloroacetanilide herbicides, including alachlor, acetochlor, and butachlor. The enzyme is a Rieske non-heme iron oxygenase, and requires a ferredoxin and EC 1.18.1.3, ferredoxin-NAD⁺ reductase, for activity.

References:

1. Chen, Q., Wang, C.H., Deng, S.K., Wu, Y.D., Li, Y., Yao, L., Jiang, J.D., Yan, X., He, J. and Li, S.P. Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2. Appl. Environ. Microbiol. 80 (2014) 5078-5085. [PMID: 24928877]

EC 1.14.18.9

Accepted name: methylsterol monooxygenase

Reaction: 4,4-dimethyl-5α-cholest-7-en-3β-ol + 6 ferrocytochrome b₅ + 3 O₂ + 6 H⁺ = 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carboxylate + 6 ferricytochrome b₅ + 4 H₂O (overall reaction)
(1a) 4,4-dimethyl-5α-cholest-7-en-3β-ol + 2 ferrocytochrome b₅ + O₂ + 2 H⁺ = 4β-hydroxymethyl-4α-methyl-5α-cholest-7-en-3β-ol + 2 ferricytochrome b₅ + H₂O
(1b) 4β-hydroxymethyl-4α-methyl-5α-cholest-7-en-3β-ol + 2 ferrocytochrome b₅ + O₂ + 2 H⁺ = 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carbaldehyde + 2 ferricytochrome b₅ + 2 H₂O
(1c) 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carbaldehyde + 2 ferrocytochrome b₅ + O₂ + 2 H⁺ = 3β-hydroxy-4β-methyl-5α-cholest-7-ene-4α-carboxylate + 2 ferricytochrome b₅ + H₂O

For diagram of reaction click here

Other name(s): methylsterol hydroxylase; 4-methylsterol oxidase; 4,4-dimethyl-5α-cholest-7-en-3β-ol,hydrogen-donor:oxygen oxidoreductase (hydroxylating)

Systematic name: 4,4-dimethyl-5α-cholest-7-en-3β-ol,ferrocytochrome-b₅:oxygen oxidoreductase (hydroxylating)

Comments: Also acts on 4α-methyl-5α-cholest-7-en-3β-ol. The sterol can be based on cycloartenol as well as lanosterol.

References:

1. Miller, W.L., Kalafer, M.E., Gaylor, J.L. and Delwicke, C.V. Investigation of the component reactions of oxidative sterol demethylation. Study of the aerobic and anaerobic processes. Biochemistry 6 (1967) 2673-2678. [PMID: 4383278]

2. Gaylor, J.L. and Mason, H.S. Investigation of the component reactions of oxidative sterol demethylation. Evidence against participation of cytochrome P-450. J. Biol. Chem. 243 (1968) 4966-4972. [PMID: 4234469]

3. Brady, D.R., Crowder, R.D. and Hayes, W.J. Mixed function oxidases in sterol metabolism. Source of reducing equivalents. J. Biol. Chem. 255 (1980) 10624-10629. [PMID: 7430141]

4. Fukushima, H., Grinstead, G.F. and Gaylor, J.L. Total enzymic synthesis of cholesterol from lanosterol. Cytochrome b₅-dependence of 4-methyl sterol oxidase. J. Biol. Chem. 256 (1981) 4822-4826. [PMID: 7228857]

5. Kawata, S., Trzaskos, J.M. and Gaylor, J.L. Affinity chromatography of microsomal enzymes on immobilized detergent-solubilized cytochrome b₅. J. Biol. Chem. 261 (1986) 3790-3799. [PMID: 3949790]

6. Pascal, S., Taton, M. and Rahier, A. Plant sterol biosynthesis. Identification and characterization of two distinct microsomal oxidative enzymatic systems involved in sterol C4-demethylation. J. Biol. Chem. 268 (1993) 11639-11654. [PMID: 8505296]

7. Rahier, A., Smith, M. and Taton, M. The role of cytochrome b₅ in 4α-methyl-oxidation and C5(6) desaturation of plant sterol precursors. Biochem. Biophys. Res. Commun. 236 (1997) 434-437. [PMID: 9240456]

EC 1.14.19.52

Accepted name: camalexin synthase

Reaction: 2-(L-cystein-S-yl)-2-(1H-indol-3-yl)acetonitrile + 2 [reduced NADPH —hemoprotein reductase] + 2 O₂ = camalexin + hydrogen cyanide + CO₂ + 2 [oxidized NADPH —hemoprotein reductase] + 4 H₂O (overall reaction)
(1a) 2-(L-cystein-S-yl)-2-(1H-indol-3-yl)acetonitrile + [reduced NADPH —hemoprotein reductase] + O₂ = (R)-dihydrocamalexate + hydrogen cyanide + [oxidized NADPH —hemoprotein reductase] + 2 H₂O
(1b) (R)-dihydrocamalexate + [reduced NADPH —hemoprotein reductase] + O₂ = camalexin + CO₂ + [oxidized NADPH —hemoprotein reductase] + 2 H₂O

Glossary: camalexin = 3-(thiazol-2-yl)indole
(R)-dihydrocamalexate = (4R)-2-(1H-indol-3-yl)-4,5-dihydrothiazole-4-carboxylate

Other name(s): CYP71B15 (gene name); bifunctional dihydrocamalexate synthase/camalexin synthase

Systematic name: 2-(cystein-S-yl)-2-(1H-indol-3-yl)-acetonitrile, [reduced NADPH —hemoprotein reductase]:oxygen oxidoreductase (camalexin-forming)

Comments: This cytochrome P-450 (heme thiolate) enzyme, which has been characterized from the plant Arabidopsis thaliana, catalyses the last two steps in the biosynthesis of camalexin, the main phytoalexin in that plant. The enzyme catalyses two successive oxidation events. During the first oxidation the enzyme introduces a C-N double bond, liberating hydrogen cyanide, and during the second oxidation it catalyses a decarboxylation.

References:

1. Schuhegger, R., Nafisi, M., Mansourova, M., Petersen, B.L., Olsen, C.E., Svatos, A., Halkier, B.A. and Glawischnig, E. CYP71B15 (PAD3) catalyzes the final step in camalexin biosynthesis. Plant Physiol. 141 (2006) 1248-1254. [PMID: 16766671]

2. Böttcher, C., Westphal, L., Schmotz, C., Prade, E., Scheel, D. and Glawischnig, E. The multifunctional enzyme CYP71B15 (PHYTOALEXIN DEFICIENT3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3-acetonitrile metabolic network of Arabidopsis thaliana. Plant Cell 21 (2009) 1830-1845. [PMID: 19567706]

EC 1.14.99.58

Accepted name: heme oxygenase (biliverdin-IX-β and δ-forming)

Reaction: (1) protoheme + 3 reduced acceptor + 3 O₂ = biliverdin-IX-δ + CO + Fe²⁺ + 3 acceptor + 3 H₂O
(2) protoheme + 3 reduced acceptor + 3 O₂ = biliverdin-IX-β + CO + Fe²⁺ + 3 acceptor + 3 H₂O

For diagram of reaction click here

Glossary: biliverdin-IX-β = 3,7-bis(2-carboxyethyl)-2,8,12,17-tetramethyl-13,18-divinylbilin-1,19(21H,24H)-dione
biliverdin-IX-δ = 3,7-bis(2-carboxyethyl)-2,8,13,18-tetramethyl-12,17-divinylbilin-1,19(21H,24H)-dione

Other name(s): pigA (gene name)

Systematic name: protoheme,donor:oxygen oxidoreductase (biliverdin-IX-β and δ-forming)

Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, differs from EC 1.14.15.20, heme oxygenase (biliverdin-producing, ferredoxin), in that the heme substrate is rotated by approximately 110 degrees within the active site, resulting in cleavage at a different part of the ring. It forms a mixture of about 70% biliverdin-IX-δ and 30% biliverdin-IX-β.

References:

1. Ratliff, M., Zhu, W., Deshmukh, R., Wilks, A. and Stojiljkovic, I. Homologues of neisserial heme oxygenase in gram-negative bacteria: degradation of heme by the product of the pigA gene of Pseudomonas aeruginosa. J. Bacteriol. 183 (2001) 6394-6403. [PMID: 11591684]

2. Caignan, G.A., Deshmukh, R., Wilks, A., Zeng, Y., Huang, H.W., Moenne-Loccoz, P., Bunce, R.A., Eastman, M.A. and Rivera, M. Oxidation of heme to β- and δ-biliverdin by Pseudomonas aeruginosa heme oxygenase as a consequence of an unusual seating of the heme. J. Am. Chem. Soc. 124 (2002) 14879-14892. [PMID: 12475329]

3. Friedman, J., Lad, L., Li, H., Wilks, A. and Poulos, T.L. Structural basis for novel δ-regioselective heme oxygenation in the opportunistic pathogen Pseudomonas aeruginosa. Biochemistry 43 (2004) 5239-5245. [PMID: 15122889]

EC 1.16.3.3

Accepted name: manganese oxidase

Reaction: 4 Mn²⁺ + 2 O₂ + 4 H₂O = 4 Mn^IVO₂ + 8 H⁺ (overall reaction)
(1a) 4 Mn²⁺ + O₂ + 4 H⁺ = 4 Mn³⁺ + 2 H₂O
(1b) 4 Mn³⁺ + O₂ + 6 H₂O = 4 Mn^IVO₂ + 12 H⁺

Other name(s): mnxG (gene name); mofA (gene name); moxA (gene name); cotA (gene name)

Systematic name: manganese(II):oxygen oxidoreductase

Comments: The enzyme, which belongs to the multicopper oxidase family, is found in many bacterial strains. It oxidizes soluble manganese(II) to insoluble manganese(IV) oxides. Since the enzyme is localized to the outer surface of the cell, its activity usually results in encrustation of the cells by the oxides. The physiological function of bacterial manganese(II) oxidation remains unclear.

References:

1. Corstjens, P.L.A.M., de Vrind, J.P.M., Goosen, T. and de Vrind-de Jong, E.W. Identification and molecular analysis of the Leptothrix discophora SS-1 mofA gene, a gene putatively encoding a manganese-oxidizing protein with copper domains. Geomicrobiol. J. 14 (1997) 91-108.

2. Francis, C.A., Casciotti, K.L. and Tebo, B.M. Localization of Mn(II)-oxidizing activity and the putative multicopper oxidase, MnxG, to the exosporium of the marine Bacillus sp. strain SG-1. Arch. Microbiol. 178 (2002) 450-456. [PMID: 12420165]

3. Ridge, J.P., Lin, M., Larsen, E.I., Fegan, M., McEwan, A.G. and Sly, L.I. A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067. Environ Microbiol 9 (2007) 944-953. [PMID: 17359266]

4. Geszvain, K., McCarthy, J.K. and Tebo, B.M. Elimination of manganese(II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes. Appl. Environ. Microbiol. 79 (2013) 357-366. [PMID: 23124227]

5. Su, J., Bao, P., Bai, T., Deng, L., Wu, H., Liu, F. and He, J. CotA, a multicopper oxidase from Bacillus pumilus WH4, exhibits manganese-oxidase activity. PLoS One 8 (2013) e60573. [PMID: 23577125]

EC 1.17.1.9

Accepted name: formate dehydrogenase

Reaction: formate + NAD⁺ = CO₂ + NADH

Other name(s): formate-NAD⁺ oxidoreductase; FDH I; FDH II; N-FDH; formic hydrogen-lyase; formate hydrogenlyase; hydrogenlyase; NAD⁺-linked formate dehydrogenase; NAD⁺-dependent formate dehydrogenase; formate dehydrogenase (NAD⁺); NAD⁺-formate dehydrogenase; formate benzyl-viologen oxidoreductase; formic acid dehydrogenase

Systematic name: formate:NAD⁺ oxidoreductase

Comments: The enzyme from most aerobic organisms is devoid of redox-active centres but that from the proteobacterium Methylosinus trichosporium contains iron-sulfur centres, flavin and a molybdenum centre [3]. Together with EC 1.12.1.2 hydrogen dehydrogenase, forms a system previously known as formate hydrogenlyase.

References:

1. Davison, D.C. Studies on plant formic dehydrogenase. Biochem. J. 49 (1951) 520-526. [PMID: 14886318]

2. Quayle, J.R. Formate dehydrogenase. Methods Enzymol. 9 (1966) 360-364.

3. Jollie, D.R. and Lipscomb, J.D. Formate dehydrogenase from Methylosinus trichosporium OB3b. Purification and spectroscopic characterization of the cofactors. J. Biol. Chem. 266 (1991) 21853-21863. [PMID: 1657982]

EC 1.17.1.10

Accepted name: formate dehydrogenase (NADP⁺)

Reaction: formate + NADP⁺ = CO₂ + NADPH

Other name(s): NADP⁺-dependent formate dehydrogenase

Systematic name: formate:NADP⁺ oxidoreductase

Comments: A tungsten-selenium-iron protein characterized from the bacterium Moorella thermoacetica. It is extremely sensitive to oxygen.

References:

1. Andreesen, J.R. and Ljungdahl, L.G. Nicotinamide adenine dinucleotide phosphate-dependent formate dehydrogenase from Clostridium thermoaceticum: purification and properties. J. Bacteriol. 120 (1974) 6-14. [PMID: 4154039]

2. Yamamoto, I., Saiki, T., Liu, S.-M. and Ljungdahl, L.G. Purification and properties of NADP-dependent formate dehydrogenase from Clostridium thermoaceticum, a tungsten-selenium-iron protein. J. Biol. Chem. 258 (1983) 1826-1832. [PMID: 6822536]

EC 1.17.1.11

Accepted name: formate dehydrogenase (NAD⁺, ferredoxin)

Reaction: 2 formate + NAD⁺ + 2 oxidized ferredoxin [iron-sulfur] cluster = 2 CO₂ + NADH + H⁺ + 2 reduced ferredoxin [iron-sulfur] cluster

Other name(s): electron-bifurcating formate dehydrogenase

Systematic name: formate:NAD⁺, ferredoxin oxidoreductase

Comments: The enzyme complex, isolated from the bacterium Gottschalkia acidurici, couples the reduction of NAD⁺ and the reduction of ferredoxin with formate via flavin-based electron bifurcation.

References:

1. Wang, S., Huang, H., Kahnt, J. and Thauer, R.K. Clostridium acidurici electron-bifurcating formate dehydrogenase. Appl. Environ. Microbiol. 79 (2013) 6176-6179. [PMID: 23872566]

EC 1.17.2.3

Accepted name: formate dehydrogenase (cytochrome-c-553)

Reaction: formate + 2 ferricytochrome c-553 = CO₂ + 2 ferrocytochrome c-553 + H⁺

Systematic name: formate:ferricytochrome-c-553 oxidoreductase

Comments: The enzyme has been characterized from the bacterium Desulfovibrio vulgaris. In vitro, yeast cytochrome c, ferricyanide and phenazine methosulfate can act as acceptors.

References:

1. Yagi, T. Formate: cytochrome oxidoreductase of Desulfovibrio vulgaris. J. Biochem. (Tokyo) 66 (1969) 473-478. [PMID: 4982127]

2. Yagi, T. Purification and properties of cytochrome c-553, an electron acceptor for formate dehydrogenase of Desulfovibrio vulgaris, Miyazaki. Biochim. Biophys. Acta 548 (1979) 96-105. [PMID: 226135]

EC 1.17.5.3

Accepted name: formate dehydrogenase-N

Reaction: formate + a quinone = CO₂ + a quinol

Other name(s): Fdh-N; FdnGHI; nitrate-inducible formate dehydrogenase; formate dehydrogenase N; FDH-N; nitrate inducible Fdn; nitrate inducible formate dehydrogenase

Systematic name: formate:quinone oxidoreductase

Comments: The enzyme contains molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters and two heme b groups. Formate dehydrogenase-N oxidizes formate in the periplasm, transferring electrons via the menaquinone pool in the cytoplasmic membrane to a dissimilatory nitrate reductase (EC 1.7.5.1), which transfers electrons to nitrate in the cytoplasm. The system generates proton motive force under anaerobic conditions [3].

References:

1. Enoch, H.G. and Lester, R.L. The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J. Biol. Chem. 250 (1975) 6693-6705. [PMID: 1099093]

2. Jormakka, M., Tornroth, S., Byrne, B. and Iwata, S. Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295 (2002) 1863-1868. [PMID: 11884747]

3. Jormakka, M., Tornroth, S., Abramson, J., Byrne, B. and Iwata, S. Purification and crystallization of the respiratory complex formate dehydrogenase-N from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 160-162. [PMID: 11752799]

EC 1.17.98.3

Accepted name: formate dehydrogenase (coenzyme F₄₂₀)

Reaction: formate + oxidized coenzyme F₄₂₀ = CO₂ + reduced coenzyme F₄₂₀

Other name(s): coenzyme F₄₂₀ reducing formate dehydrogenase; coenzyme F₄₂₀-dependent formate dehydrogenase

Systematic name: formate:coenzyme-F₄₂₀ oxidoreductase

Comments: The enzyme, characterized from methanogenic archaea, is involved in formate-dependent H₂ production. It contains noncovalently bound FAD [1].

References:

1. Schauer, N.L. and Ferry, J.G. FAD requirement for the reduction of coenzyme F₄₂₀ by formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 155 (1983) 467-472. [PMID: 6874636]

2. Schauer, N.L. and Ferry, J.G. Composition of the coenzyme F₄₂₀-dependent formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 165 (1986) 405-411. [PMID: 3944055]

3. Lupa, B., Hendrickson, E.L., Leigh, J.A. and Whitman, W.B. Formate-dependent H₂ production by the mesophilic methanogen Methanococcus maripaludis. Appl. Environ. Microbiol. 74 (2008) 6584-6590. [PMID: 18791018]

EC 1.17.99.7

Accepted name: formate dehydrogenase (acceptor)

Reaction: formate + acceptor = CO₂ + reduced acceptor

Other name(s): FDHH; FDH-H; FDH-O; formate dehydrogenase H; formate dehydrogenase O

Systematic name: formate:acceptor oxidoreductase

Comments: Formate dehydrogenase H is a cytoplasmic enzyme that oxidizes formate without oxygen transfer, transferring electrons to a hydrogenase. The two enzymes form the formate-hydrogen lyase complex [1]. The enzyme contains an [4Fe-4S] cluster, a selenocysteine residue and a molybdopterin cofactor [1].

References:

1. Axley, M.J., Grahame, D.A. and Stadtman, T.C. Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component. J. Biol. Chem. 265 (1990) 18213-18218. [PMID: 2211698]

2. Gladyshev, V.N., Boyington, J.C., Khangulov, S.V., Grahame, D.A., Stadtman, T.C. and Sun, P.D. Characterization of crystalline formate dehydrogenase H from Escherichia coli. Stabilization, EPR spectroscopy, and preliminary crystallographic analysis. J. Biol. Chem. 271 (1996) 8095-8100. [PMID: 8626495]

3. Khangulov, S.V., Gladyshev, V.N., Dismukes, G.C. and Stadtman, T.C. Selenium-containing formate dehydrogenase H from Escherichia coli: a molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer. Biochemistry 37 (1998) 3518-3528. [PMID: 9521673]

EC 2.1.1.343

Accepted name: 8-amino-8-demethylriboflavin N,N-dimethyltransferase

Reaction: 2 S-adenosyl-L-methionine + 8-amino-8-demethylriboflavin = 2 S-adenosyl-L-homocysteine + roseoflavin (overall reaction)
(1a) S-adenosyl-L-methionine + 8-amino-8-demethylriboflavin = S-adenosyl-L-homocysteine + 8-demethyl-8-(methylamino)riboflavin
(1b) S-adenosyl-L-methionine + 8-demethyl-8-(methylamino)riboflavin = S-adenosyl-L-homocysteine + roseoflavin

Glossary: roseoflavin = 8-demethyl-8-(dimethylamino)riboflavin

Other name(s): rosA (gene name)

Systematic name: S-adenosyl-L-methionine:8-amino-8-demethylriboflavin N,N-dimethyltransferase

Comments: The enzyme, characterized from the soil bacterium Streptomyces davawensis, catalyses the last two steps in the biosynthesis of the antibiotic roseoflavin.

References:

1. Jankowitsch, F., Kuhm, C., Kellner, R., Kalinowski, J., Pelzer, S., Macheroux, P. and Mack, M. A novel N,N-8-amino-8-demethyl-D-riboflavin dimethyltransferase (RosA) catalyzing the two terminal steps of roseoflavin biosynthesis in Streptomyces davawensis. J. Biol. Chem. 286 (2011) 38275-38285. [PMID: 21911488]

2. Tongsook, C., Uhl, M.K., Jankowitsch, F., Mack, M., Gruber, K. and Macheroux, P. Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-D-riboflavin to the antibiotic roseoflavin. FEBS J. 283 (2016) 1531-1549. [PMID: 26913589]

EC 2.1.1.344

Accepted name: ornithine lipid N-methyltransferase

Reaction: 3 S-adenosyl-L-methionine + an ornithine lipid = 3 S-adenosyl-L-homocysteine + an N,N,N-trimethylornithine lipid (overall reaction)
(1a) S-adenosyl-L-methionine + an ornithine lipid = S-adenosyl-L-homocysteine + an N-methylornithine lipid
(1b) S-adenosyl-L-methionine + an N-methylornithine lipid = S-adenosyl-L-homocysteine + an N,N-dimethylornithine lipid
(1c) S-adenosyl-L-methionine + an N,N-dimethylornithine lipid = S-adenosyl-L-homocysteine + an N,N,N-trimethylornithine lipid

Glossary: an ornithine lipid = an N^α-[(3R)-3-(acyloxy)acyl]-L-ornithine

Other name(s): olsG (gene name)

Systematic name: S-adenosyl-L-methionine:ornithine lipid N-methyltransferase

Comments: The enzyme, characterized from the bacterium Singulisphaera acidiphila, catalyses three successive methylations of the terminal δ-nitrogen in ornithine lipids.

References:

1. Escobedo-Hinojosa, W.I., Vences-Guzman, M.A., Schubotz, F., Sandoval-Calderon, M., Summons, R.E., Lopez-Lara, I.M., Geiger, O. and Sohlenkamp, C. OlsG (Sinac_1600) is an ornithine lipid N-methyltransferase from the planctomycete Singulisphaera acidiphila. J. Biol. Chem. 290 (2015) 15102-15111. [PMID: 25925947]

EC 2.3.1.265

Accepted name: phosphatidylinositol dimannoside acyltransferase

Reaction: (1) an acyl-CoA + 2,6-di-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol = CoA + 2-O-(6-O-acyl-α-D-mannosyl)-6-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol
(2) an acyl-CoA + 2-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol = CoA + 2-O-(6-O-acyl-α-D-mannosyl)-1-phosphatidyl-1D-myo-inositol

Other name(s): PIM2 acyltransferase; ptfP1 (gene name)

Systematic name: acyl-CoA:2,6-di-O-α-D-mannosyl-1-phosphatidyl-1D-myo-inositol acyltransferase

Comments: The enzyme, found in Corynebacteriales, is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs).

References:

1. Svetlikova, Z., Barath, P., Jackson, M., Kordulakova, J. and Mikusova, K. Purification and characterization of the acyltransferase involved in biosynthesis of the major mycobacterial cell envelope glycolipid —monoacylated phosphatidylinositol dimannoside. Protein Expr. Purif. 100 (2014) 33-39. [PMID: 24810911]

[EC 2.3.2.4 Transferred entry: γ-glutamylcyclotransferase. Now classified as EC 4.3.2.9, γ-glutamylcyclotransferase (EC 2.3.2.4 created 1972, deleted 2017)]

EC 2.3.2.30

Accepted name: L-ornithine N^α-acyltransferase

Reaction: L-ornithine + a (3R)-3-hydroxyacyl-[acyl-carrier protein] = a lyso-ornithine lipid + a holo-[acyl-carrier protein]

Glossary: a lyso-ornithine lipid = an N^α-[(3R)-hydroxy-acyl]-L-ornithine

Other name(s): olsB (gene name)

Systematic name: L-ornithine N^α-(3R)-3-hydroxy-acyltransferase

Comments: The enzyme, found in bacteria, catalyses the first step in the biosynthesis of ornithine lipids.

References:

1. Gao, J.L., Weissenmayer, B., Taylor, A.M., Thomas-Oates, J., Lopez-Lara, I.M. and Geiger, O. Identification of a gene required for the formation of lyso-ornithine lipid, an intermediate in the biosynthesis of ornithine-containing lipids. Mol. Microbiol. 53 (2004) 1757-1770. [PMID: 15341653]

2. Vences-Guzman, M.A., Guan, Z., Bermudez-Barrientos, J.R., Geiger, O. and Sohlenkamp, C. Agrobacteria lacking ornithine lipids induce more rapid tumour formation. Environ Microbiol 15 (2013) 895-906. [PMID: 22958119]

*EC 2.4.1.52

Accepted name: poly(glycerol-phosphate) α-glucosyltransferase

Reaction: n UDP-α-D-glucose + 4-O-{poly[(2R)-glycerophospho]-(2R)-glycerophospho}-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = n UDP + 4-O-{poly[(2R)-2-α-D-glucosyl-1-glycerophospho]-(2R)-glycerophospho}-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol

Other name(s): UDP glucose-poly(glycerol-phosphate) α-glucosyltransferase; uridine diphosphoglucose-poly(glycerol-phosphate) α-glucosyltransferase; tagE (gene name); UDP-glucose:poly(glycerol-phosphate) α-D-glucosyltransferase

Systematic name: UDP-α-D-glucose:4-O-{poly[(2R)-glycerophospho]-(2R)-glycerophospho}-N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol α-D-glucosyltransferase (configuration-retaining)

Comments: Involved in the biosynthesis of poly glycerol phosphate teichoic acids in bacterial cell walls. This enzyme, isolated from Bacillus subtilis 168, adds an α-D-glucose to the free OH groups of the glycerol units. The enzyme has a strong preference for UDP-α-glucose as the sugar donor. It has no activity with poly(ribitol phosphate).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37277-60-4

References:

1. Glaser, L. and Burger, M.M. The synthesis of teichoic acids. 3. Glucosylation of polyglycerophosphate. J. Biol. Chem. 239 (1964) 3187-3191. [PMID: 14245359]

2. Allison, S.E., D'Elia, M.A., Arar, S., Monteiro, M.A. and Brown, E.D. Studies of the genetics, function, and kinetic mechanism of TagE, the wall teichoic acid glycosyltransferase in Bacillus subtilis 168. J. Biol. Chem. 286 (2011) 23708-23716. [PMID: 21558268]

*EC 2.4.1.150

Accepted name: N-acetyllactosaminide β-1,6-N-acetylglucosaminyltransferase

Reaction: UDP-N-acetyl-α-D-glucosamine + β-D-Gal-(1→4)-β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-GlcNAc-R = UDP + β-D-Gal-(1→4)-β-D-GlcNAc-(1→3)-[β-D-GlcNAc-(1→6)]-β-D-Gal-(1→4)-β-D-GlcNAc-R

Glossary: β-D-galactosyl-(1→4)-N-acetyl-D-glucosaminyl-R = type 2 precursor disaccharide

Other name(s): GCNT2 (gene name); GCNT3 (gene name); IGnT; I-branching β1,6-N-acetylglucosaminyltransferase; N-acetylglucosaminyltransferase; uridine diphosphoacetylglucosamine-acetyllactosaminide β1→6-acetylglucosaminyltransferase; Galβ1→4GlcNAc-R β1→6 N-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:β-D-galactosyl-1,4-N-acetyl-D-glucosaminide β-1,6-N-acetyl-D-glucosaminyltransferase

Systematic name: UDP-N-acetyl-α-D-glucosamine:β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminide 6-β-N-acetylglucosaminyltransferase (configuration-inverting)

Comments: The enzyme acts on poly-N-acetyllactosamine [glycan chains of β-D-galactosyl-(1→4)-N-acetyl-D-glucosamine units connected by β(1,3) linkages] attached to proteins or lipids. It transfers a GlcNAc residue by β(1,6)-linkage to galactosyl residues close to non-reducing terminals, introducing a branching pattern known as I branching.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 85638-40-0

References:

1. Van den Eijnden, D.H., Winterwerp, H., Smeeman, P. and Schiphorst, W.E.C.M. Novikoff ascites tumor cells contain N-acetyllactosaminide β1→3 and β1→6 N-acetylglucosaminyltransferase activity. J. Biol. Chem. 258 (1983) 3435-3437. [PMID: 6219989]

2. Basu, M. and Basu, S. Biosynthesis in vitro of Ii core glycosphingolipids from neolactotetraosylceramide by β 1-3- and β 1-6-N-acetylglucosaminyltransferases from mouse T-lymphoma. J. Biol. Chem. 259 (1984) 12557-12562. [PMID: 6238026]

3. Piller, F., Cartron, J.P., Maranduba, A., Veyrieres, A., Leroy, Y. and Fournet, B. Biosynthesis of blood group I antigens. Identification of a UDP-GlcNAc:GlcNAc β 1-3Gal(-R) β 1-6(GlcNAc to Gal) N-acetylglucosaminyltransferase in hog gastric mucosa. J. Biol. Chem. 259 (1984) 13385-13390. [PMID: 6490658]

4. Bierhuizen, M.F., Maemura, K., Kudo, S. and Fukuda, M. Genomic organization of core 2 and I branching β-1,6-N-acetylglucosaminyltransferases. Implication for evolution of the β-1,6-N-acetylglucosaminyltransferase gene family. Glycobiology 5 (1995) 417-425. [PMID: 7579796]

5. Ujita, M., McAuliffe, J., Suzuki, M., Hindsgaul, O., Clausen, H., Fukuda, M.N. and Fukuda, M. Regulation of I-branched poly-N-acetyllactosamine synthesis. Concerted actions by I-extension enzyme, I-branching enzyme, and β1,4-galactosyltransferase I. J. Biol. Chem. 274 (1999) 9296-9304. [PMID: 10092606]

6. Yeh, J.C., Ong, E. and Fukuda, M. Molecular cloning and expression of a novel β-1, 6-N-acetylglucosaminyltransferase that forms core 2, core 4, and I branches. J. Biol. Chem. 274 (1999) 3215-3221. [PMID: 9915862]

[EC 2.4.1.164 Transferred entry: galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide β-1,6-N-acetylglucosaminyltransferase, now included with EC 2.4.1.150, N-acetyllactosaminide β-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.164 created 1989, deleted 2016)]

EC 2.4.1.347

Accepted name: α,α-trehalose-phosphate synthase (ADP-forming)

Reaction: ADP-α-D-glucose + D-glucose 6-phosphate = ADP + α,α-trehalose 6-phosphate

Other name(s): otsA (gene name); ADP-glucose —glucose-phosphate glucosyltransferase

Systematic name: ADP-α-D-glucose:D-glucose-6-phosphate 1-α-D-glucosyltransferase (configuration-retaining)

Comments: The enzyme has been reported from the yeast Saccharomyces cerevisiae and from mycobacteria. The enzyme from Mycobacterium tuberculosis can also use UDP-α-D-glucose, but the activity with ADP-α-D-glucose, which is considered the main substrate in vivo, is higher.

References:

1. Ferreira, J.C., Thevelein, J.M., Hohmann, S., Paschoalin, V.M., Trugo, L.C. and Panek, A.D. Trehalose accumulation in mutants of Saccharomyces cerevisiae deleted in the UDPG-dependent trehalose synthase-phosphatase complex. Biochim. Biophys. Acta 1335 (1997) 40-50. [PMID: 9133641]

2. Pan, Y.T., Carroll, J.D. and Elbein, A.D. Trehalose-phosphate synthase of Mycobacterium tuberculosis. Cloning, expression and properties of the recombinant enzyme. Eur. J. Biochem. 269 (2002) 6091-6100. [PMID: 12473104]

3. Asencion Diez, M.D., Demonte, A.M., Syson, K., Arias, D.G., Gorelik, A., Guerrero, S.A., Bornemann, S. and Iglesias, A.A. Allosteric regulation of the partitioning of glucose-1-phosphate between glycogen and trehalose biosynthesis in Mycobacterium tuberculosis. Biochim. Biophys. Acta 1850 (2015) 13-21. [PMID: 25277548]

EC 2.5.1.141

Accepted name: heme o synthase

Reaction: (2E,6E)-farnesyl diphosphate + protoheme IX + H₂O = diphosphate + ferroheme o

For diagram of reaction click here

Other name(s): ctaB (gene name); COX10 (gene name)

Systematic name: (2E,6E)-farnesyl-diphosphate:protoheme IX farnesyltranstransferase

Comments: The enzyme, found in many archaea, bacteria, and eukaryotes, produces heme o, which in many cases is further modified into heme a. In organisms that produce heme a, the enzyme forms a complex with heme a synthase.

References:

1. Saiki, K., Mogi, T. and Anraku, Y. Heme O biosynthesis in Escherichia coli: the cyoE gene in the cytochrome bo operon encodes a protoheme IX farnesyltransferase. Biochem. Biophys. Res. Commun. 189 (1992) 1491-1497. [PMID: 1336371]

2. Svensson, B., Lubben, M. and Hederstedt, L. Bacillus subtilis CtaA and CtaB function in haem A biosynthesis. Mol. Microbiol. 10 (1993) 193-201. [PMID: 7968515]

3. Glerum, D.M. and Tzagoloff, A. Isolation of a human cDNA for heme A:farnesyltransferase by functional complementation of a yeast cox10 mutant. Proc. Natl. Acad. Sci. USA 91 (1994) 8452-8456. [PMID: 8078902]

4. Brown, B.M., Wang, Z., Brown, K.R., Cricco, J.A. and Hegg, E.L. Heme O synthase and heme A synthase from Bacillus subtilis and Rhodobacter sphaeroides interact in Escherichia coli. Biochemistry 43 (2004) 13541-13548. [PMID: 15491161]

5. Mogi, T. Over-expression and characterization of Bacillus subtilis heme O synthase. J. Biochem. 145 (2009) 669-675. [PMID: 19204012]

EC 2.7.1.218

Accepted name: fructoselysine 6-kinase

Reaction: ATP + N⁶-(D-fructosyl)-L-lysine = ADP + N⁶-(6-phospho-D-fructosyl)-L-lysine

Other name(s): frlD (gene name)

Systematic name: ATP:D-fructosyl-L-lysine 6-phosphotransferase

Comments: The enzyme, characterized from the bacterium Escherichia coli, has very little activity with fructose.

References:

1. Wiame, E., Delpierre, G., Collard, F. and Van Schaftingen, E. Identification of a pathway for the utilization of the Amadori product fructoselysine in Escherichia coli. J. Biol. Chem. 277 (2002) 42523-42529. [PMID: 12147680]

2. Wiame, E. and Van Schaftingen, E. Fructoselysine 3-epimerase, an enzyme involved in the metabolism of the unusual Amadori compound psicoselysine in Escherichia coli. Biochem. J. 378 (2004) 1047-1052. [PMID: 14641112]

EC 2.7.1.219<

Accepted name: D-threonate 4-kinase

Reaction: ATP + D-threonate = ADP + 4-phospho-D-threonate

For diagram of reaction click here

Glossary: D-threonate = (2S,3R)-2,3,4-trihydroxybutanoate

Other name(s): dtnK (gene name)

Systematic name: ATP:D-threonate 4-phosphotransferase

Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-threonate catabolism.

References:

1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]

EC 2.7.1.220

Accepted name: D-erythronate 4-kinase

Reaction: ATP + D-erythronate = ADP + 4-phospho-D-erythronate

For diagram of reaction click here

Glossary: D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s): denK (gene name)

Systematic name: ATP:D-erythronate 4-phosphotransferase

Comments: The enzyme, characterized from bacteria, is involved in a pathway for D-erythronate catabolism.

References:

1. Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl Acad. Sci. USA 113 (2016) E4161-E4169. [PMID: 27402745]

EC 2.7.1.221

Accepted name: N-acetylmuramate 1-kinase

Reaction: ATP + N-acetyl-D-muramate = ADP + N-acetyl-α-D-muramate 1-phosphate

Glossary: N-acetyl-D-muramate = 3-O-[(1R)-1-carboxyethyl]-2-acetoxy-2-deoxy-D-glucopyranose

Other name(s): amgK (gene name)

Systematic name: ATP:N-acetyl-D-muramate 1-phosphotransferase

Comments: The enzyme, characterized from Pseudomonas species, participates in a peptidoglycan salvage pathway.

References:

1. Gisin, J., Schneider, A., Nagele, B., Borisova, M. and Mayer, C. A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis. Nat. Chem. Biol. 9 (2013) 491-493. [PMID: 23831760]

[EC 2.7.7.98 Transferred entry: 4-hydroxybenzoate adenylyltransferase. Now EC 6.2.1.50, 4-hydroxybenzoate adenylyltransferase FadD22 (EC 2.7.7.98 created 2017, deleted 2017)]

EC 2.7.7.99

Accepted name: N-acetyl-α-D-muramate 1-phosphate uridylyltransferase

Reaction: UDP + N-acetyl-α-D-muramate 1-phosphate = UDP-N-acetyl-α-D-muramate + phosphate

Glossary: N-acetyl-D-muramate = 3-O-[(1R)-1-carboxyethyl]-2-acetoxy-2-deoxy-D-glucopyranose

Other name(s): murU (gene name)

Systematic name: UDP:N-acetyl-α-D-muramate 1-phosphate uridylyltransferase

Comments: The enzyme, characterized from Pseudomonas species, participates in a peptidoglycan salvage pathway.

References:

1. Gisin, J., Schneider, A., Nagele, B., Borisova, M. and Mayer, C. A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis. Nat. Chem. Biol. 9 (2013) 491-493. [PMID: 23831760]

2. Renner-Schneck, M., Hinderberger, I., Gisin, J., Exner, T., Mayer, C. and Stehle, T. Crystal structure of the N-acetylmuramic acid α-1-phosphate (MurNAc-α1-P) uridylyltransferase MurU, a minimal sugar nucleotidyltransferase and potential drug target enzyme in Gram-negative pathogens. J. Biol. Chem. 290 (2015) 10804-10813. [PMID: 25767118]

*EC 2.8.2.24

Accepted name: aromatic desulfoglucosinolate sulfotransferase

Reaction: (1) 3'-phosphoadenylyl sulfate + desulfoglucotropeolin = adenosine 3',5'-bisphosphate + glucotropeolin
(2) 3'-phosphoadenylyl sulfate + indolylmethyl-desulfoglucosinolate = adenosine 3',5'-bisphosphate + glucobrassicin

For diagram of reaction click here

Glossary: 3'-phosphoadenylyl sulfate = PAPS

Other name(s): desulfoglucosinolate sulfotransferase (ambiguous); PAPS-desulfoglucosinolate sulfotransferase (ambiguous); 3'-phosphoadenosine-5'-phosphosulfate:desulfoglucosinolate sulfotransferase (ambiguous)

Systematic name: 3'-phosphoadenylyl-sulfate:aromatic desulfoglucosinolate sulfotransferase

Comments: This enzyme, characterized from cruciferous plants, catalyses the last step in the biosynthesis of tryptophan- and phenylalanine-derived glucosinolates. cf. EC 2.8.2.38, aliphatic desulfoglucosinolate sulfotransferase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 121479-85-4

References:

1. Jain, J.C., Reed, D.W., Groot Wassink, J.W.D. and Underhill, E.W. A radioassay of enzymes catalyzing the glucosylation and sulfation steps of glucosinolate biosynthesis in Brassica species. Anal. Biochem. 178 (1989) 137-140. [PMID: 2524977]

2. Klein, M., Reichelt, M., Gershenzon, J. and Papenbrock, J. The three desulfoglucosinolate sulfotransferase proteins in Arabidopsis have different substrate specificities and are differentially expressed. FEBS J. 273 (2006) 122-136. [PMID: 16367753]

3. Klein, M. and Papenbrock, J. Kinetics and substrate specificities of desulfo-glucosinolate sulfotransferases in Arabidopsis thaliana. Physiol. Plant 135 (2009) 140-149. [PMID: 19077143]

EC 2.8.2.38

Accepted name: aliphatic desulfoglucosinolate sulfotransferase

Reaction: 3'-phosphoadenylyl sulfate + an aliphatic desulfoglucosinolate = adenosine 3',5'-bisphosphate + an aliphatic glucosinolate

Other name(s): SOT17 (gene name); SOT18 (gene name)

Systematic name: 3'-phosphoadenylyl-sulfate:aliphatic desulfoglucosinolate sulfotransferase

Comments: The enzyme catalyses the last step in the biosynthesis of aliphatic glucosinolate core structures. cf. EC 2.8.2.24, aromatic desulfoglucosinolate sulfotransferase.

References:

1. Piotrowski, M., Schemenewitz, A., Lopukhina, A., Muller, A., Janowitz, T., Weiler, E.W. and Oecking, C. Desulfoglucosinolate sulfotransferases from Arabidopsis thaliana catalyze the final step in the biosynthesis of the glucosinolate core structure. J. Biol. Chem. 279 (2004) 50717-50725. [PMID: 15358770]

2. Klein, M., Reichelt, M., Gershenzon, J. and Papenbrock, J. The three desulfoglucosinolate sulfotransferase proteins in Arabidopsis have different substrate specificities and are differentially expressed. FEBS J. 273 (2006) 122-136. [PMID: 16367753]

3. Klein, M. and Papenbrock, J. Kinetics and substrate specificities of desulfo-glucosinolate sulfotransferases in Arabidopsis thaliana. Physiol. Plant 135 (2009) 140-149. [PMID: 19077143]

EC 2.8.2.39

Accepted name: hydroxyjasmonate sulfotransferase

Reaction: 3'-phosphoadenylyl-sulfate + 12-hydroxyjasmonate = adenosine 3',5'-bisphosphate + 12-sulfooxyjasmonate

Glossary: 12-hydroxyjasmonate = {(1R,2R)-2-[(2E)-5-hydroxypent-2-enyl]-3-oxocyclopentyl}acetate

Other name(s): ST2A (gene name)

Systematic name: 3'-phosphoadenylyl-sulfate:12-hydroxyjasmonate sulfotransferase

Comments: The enzyme, charaterized from the plant Arabidopsis thaliana, also acts on 11-hydroxyjasmonate.

References:

1. Gidda, S.K., Miersch, O., Levitin, A., Schmidt, J., Wasternack, C. and Varin, L. Biochemical and molecular characterization of a hydroxyjasmonate sulfotransferase from Arabidopsis thaliana. J. Biol. Chem. 278 (2003) 17895-17900. [PMID: 12637544]

EC 3.1.3.105

Accepted name: N-acetyl-D-muramate 6-phosphate phosphatase

Reaction: N-acetyl-D-muramate 6-phosphate + H₂O = N-acetyl-D-muramate + phosphate

Other name(s): mupP (gene name)

Systematic name: N-acetyl-D-muramate 6-phosphate phosphohydrolase

Comments: The enzyme, characterized from Pseudomonas species, participates in a peptidoglycan salvage pathway.

References:

1. Borisova, M., Gisin, J. and Mayer, C. The N-acetylmuramic acid 6-phosphate phosphatase MupP completes the Pseudomonas peptidoglycan recycling pathway leading to intrinsic fosfomycin resistance. LID - e00092-17 [pii] LID - 10.1128/mBio.00092-17 [doi. MBio 8 (2017) . [PMID: 28351914]

EC 3.1.4.58

Accepted name: RNA 2',3'-cyclic 3'-phosphodiesterase

Reaction: (ribonucleotide)_n-2',3'-cyclic phosphate + H₂O = (ribonucleotide)_n-2'-phosphate

Other name(s): thpR (gene name); ligT (gene name)

Systematic name: (ribonucleotide)_n-2',3'-cyclic phosphate 3'-nucleotidohydrolase

Comments: The enzyme hydrolyses RNA 2',3'-cyclic phosphodiester to an RNA 2'-phosphomonoester. In vitro the enzyme can also ligate tRNA molecules with 2',3'-cyclic phosphate to tRNA with 5'-hydroxyl termini, forming a 2'-5' phosphodiester linkage. However, the ligase activity is unlikely to be relevant in vivo.

References:

1. Kanai, A., Sato, A., Fukuda, Y., Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G. and Tomita, M. Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA 15 (2009) 420-431. [PMID: 19155324]

2. Remus, B.S., Jacewicz, A. and Shuman, S. Structure and mechanism of E. coli RNA 2',3'-cyclic phosphodiesterase. RNA 20 (2014) 1697-1705. [PMID: 25239919]

[EC 3.1.7.7 Transferred entry: (–)-drimenol synthase. Now EC 4.2.3.194, (–)-drimenol synthase (EC 3.1.7.7 created 2011, deleted 2017)]

EC 3.1.7.12

Accepted name: (+)-kolavelool synthase

Reaction: (+)-kolavenyl diphosphate + H₂O = (+)-kolavelool + diphosphate

For diagram of reaction click here

Glossary: (+)-kolavelool = (2ξ)-3-methyl-5-[(1R,2S,4aS,8aS)-1,2,4a,5-tetramethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-yl]pent-1-en-3-ol

Other name(s): Haur_2146

Systematic name: kolavenyl-diphosphate diphosphohydrolase

Comments: Isolated from the bacterium Herpetosiphon aurantiacus.

References:

1. Nakano, C., Oshima, M., Kurashima, N. and Hoshino, T. Identification of a new diterpene biosynthetic gene cluster that produces O-methylkolavelool in Herpetosiphon aurantiacus. Chembiochem 16 (2015) 772-781. [PMID: 25694050]

*EC 3.2.1.130

Accepted name: glycoprotein endo-α-1,2-mannosidase

Reaction: GlcMan₉GlcNAc₂-[protein] + H₂O = Man₈GlcNAc₂-[protein] (isomer 8A_1,2,3B_1,2) + α-D-glucosyl-(1→3)-α-D-mannopyranose

Glossary: GlcMan₉GlcNAc₂-[protein] = {α-D-Glc-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]
Man₈GlcNAc₂-[protein] (isomer 8A_1,2,3B_1,2) = {α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]

Other name(s): glucosylmannosidase; endo-α-D-mannosidase; endo-α-mannosidase; endomannosidase; glucosyl mannosidase; MANEA (gene name); glycoprotein glucosylmannohydrolase

Systematic name: glycoprotein glucosylmannohydrolase (configuration-retaining)

Comments: The enzyme catalyses the hydrolysis of the terminal α-D-glucosyl-(1→3)-D-mannosyl unit from the GlcMan₉(GlcNAc)₂ oligosaccharide component of N-glucosylated proteins during their processing in the Golgi apparatus. The name for the isomer is based on a nomenclature proposed by Prien et al [7].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 108022-16-8

References:

1. Lubas, W.A. and Spiro, R.G. Golgi endo-α-D-mannosidase from rat liver, a novel N-linked carbohydrate unit processing enzyme. J. Biol. Chem. 262 (1987) 3775-3781. [PMID: 3818665]

2. Tulsiani, D.R.P., Coleman, V.P. and Touster, O. Asparagine-linked glycoprotein biosynthesis in rat brain: identification of glucosidase I, glucosidase II, and endomannosidase (glucosyl mannosidase). Arch. Biochem. Biophys. 277 (1990) 114-121. [PMID: 2407194]

3. Hiraizumi, S., Spohr, U. and Spiro, R.G. Ligand affinity chromatographic purification of rat liver Golgi endomannosidase. J. Biol. Chem. 269 (1994) 4697-4700. [PMID: 8106437]

4. Spiro, M.J., Bhoyroo, V.D. and Spiro, R.G. Molecular cloning and expression of rat liver endo-α-mannosidase, an N-linked oligosaccharide processing enzyme. J. Biol. Chem. 272 (1997) 29356-29363. [PMID: 9361017]

5. Hamilton, S.R., Li, H., Wischnewski, H., Prasad, A., Kerley-Hamilton, J.S., Mitchell, T., Walling, A.J., Davidson, R.C., Wildt, S. and Gerngross, T.U. Intact α-1,2-endomannosidase is a typical type II membrane protein. Glycobiology 15 (2005) 615-624. [PMID: 15677381]

6. Hardt, B., Volker, C., Mundt, S., Salska-Navarro, M., Hauptmann, M. and Bause, E. Human endo-α1,2-mannosidase is a Golgi-resident type II membrane protein. Biochimie 87 (2005) 169-179. [PMID: 15760709]

7. Prien, J.M., Ashline, D.J., Lapadula, A.J., Zhang, H. and Reinhold, V.N. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS. J Am Soc Mass Spectrom 20 (2009) 539-556. [PMID: 19181540]

EC 3.2.1.204

Accepted name: 1,3-α-isomaltosidase

Reaction: cyclobis-(1→6)-α-nigerosyl + 2 H₂O = 2 isomaltose (overall reaction)
(1a) cyclobis-(1→6)-α-nigerosyl + H₂O = α-isomaltosyl-(1→3)-isomaltose
(1b) α-isomaltosyl-(1→3)-isomaltose + H₂O = 2 isomaltose

Systematic name: 1,3-α-isomaltohydrolase (configuration-retaining)

Comments: The enzyme, characterized from the bacteria Bacillus sp. NRRL B-21195 and Kribbella flavida, participates in the degradation of starch. The cyclic tetrasaccharide cyclobis-(1→6)-α-nigerosyl is formed from starch extracellularly and imported into the cell, where it is degraded to glucose.

References:

1. Kim, Y.K., Kitaoka, M., Hayashi, K., Kim, C.H. and Cote, G.L. Purification and characterization of an intracellular cycloalternan-degrading enzyme from Bacillus sp. NRRL B-21195. Carbohydr. Res. 339 (2004) 1179-1184. [PMID: 15063208]

2. Tagami, T., Miyano, E., Sadahiro, J., Okuyama, M., Iwasaki, T. and Kimura, A. Two novel glycoside hydrolases responsible for the catabolism of cyclobis-(1→6)-α-nigerosyl. J. Biol. Chem. 291 (2016) 16438-16447. [PMID: 27302067]

EC 3.2.1.205

Accepted name: isomaltose glucohydrolase

Reaction: isomaltose + H₂O = β-D-glucose + D-glucose

Systematic name: isomaltose 6-α-glucohydrolase (configuration-inverting)

Comments: The enzyme catalyses the hydrolysis of α-1,6-glucosidic linkages from the non-reducing end of its substrate. Unlike EC 3.2.1.10, oligo-1,6-glucosidase, the enzyme inverts the anomeric configuration of the released residue. The enzyme can also act on panose and maltotriose at a lower rate.

References:

1. Tagami, T., Miyano, E., Sadahiro, J., Okuyama, M., Iwasaki, T. and Kimura, A. Two novel glycoside hydrolases responsible for the catabolism of cyclobis-(1→6)-α-nigerosyl. J. Biol. Chem. 291 (2016) 16438-16447. [PMID: 27302067]

EC 3.4.19.16

Accepted name: glucosinolate γ-glutamyl hydrolase

Reaction: (1) an (E)-1-(glutathion-S-yl)-N-hydroxy-ω-(methylsulfanyl)alkan-1-imine + H₂O = an (E)-1-(L-cysteinylglycin-S-yl)-N-hydroxy-ω-(methylsulfanyl)alkan-1-imine + L-glutamate
(2) (E)-1-(glutathion-S-yl)-N-hydroxy-2-(1H-indol-3-yl)ethan-1-imine + H₂O = (E)-1-(L-cysteinylglycin-S-yl)-N-hydroxy-2-(1H-indol-3-yl)ethan-1-imine + L-glutamate
(3) (glutathion-S-yl)(1H-indol-3-yl)acetonitrile + H₂O = (L-cysteinylglycin-S-yl)(1H-indol-3-yl)acetonitrile + L-glutamate
(4) (Z)-1-(glutathion-S-yl)-N-hydroxy-2-phenylethan-1-imine + H₂O = (Z)-1-(L-cysteinyglycin-S-yl)-N-hydroxy-2-phenylethan-1-imine + L-glutamate

Other name(s): GGP1 (gene name); GGP3 (gene name)

Comments: This enzyme, characterized from the plant Arabidopsis thaliana, participates in the biosynthesis of the plant defense compounds glucosinolates and camalexin. It is the only known plant enzyme capable of hydrolysing the γ-glutamyl residue of glutathione in the cytosol.

References:

1. Geu-Flores, F., Møldrup, M.E., Böttcher, C., Olsen, C.E., Scheel, D. and Halkier, B.A. Cytosolic γ-glutamyl peptidases process glutathione conjugates in the biosynthesis of glucosinolates and camalexin in Arabidopsis. Plant Cell 23 (2011) 2456-2469. [PMID: 21712415]

EC 3.13.1.6

Accepted name: [CysO sulfur-carrier protein]-S-L-cysteine hydrolase

Reaction: [CysO sulfur-carrier protein]-Gly-NH-CH₂-C(O)-S-L-cysteine + H₂O = [CysO sulfur-carrier protein]-Gly-NH-CH₂-COOH + L-cysteine

Other name(s): mec (gene name)

Systematic name: [CysO sulfur-carrier protein]-S-L-cysteine sulfohydrolase

Comments: Requires Zn²⁺. The enzyme, characterized from the bacterium Mycobacterium tuberculosis, participates in an L-cysteine biosynthesis pathway. It acts on the product of EC 2.5.1.113, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase.

References:

1. Burns, K.E., Baumgart, S., Dorrestein, P.C., Zhai, H., McLafferty, F.W. and Begley, T.P. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. J. Am. Chem. Soc. 127 (2005) 11602-11603. [PMID: 16104727]

EC 4.2.1.172

Accepted name: trans-4-hydroxy-L-proline dehydratase

Reaction: trans-4-hydroxy-L-proline = (S)-1-pyrroline-5-carboxylate + H₂O

Glossary: 1-pyrroline = 3,4-dihydro-2H-pyrrole

Systematic name: trans-4-hydroxy-L-proline hydro-lyase

Comments: The enzyme has been characterized from the bacterium Peptoclostridium difficile. The active form contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (SAM) and a [4Fe-4S] cluster.

References:

1. Levin, B.J., Huang, Y.Y., Peck, S.C., Wei, Y., Martinez-Del Campo, A., Marks, J.A., Franzosa, E.A., Huttenhower, C. and Balskus, E.P. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline. Science 355 (2017) . [PMID: 28183913]

EC 4.2.1.173

Accepted name: ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase

Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H₂O

For diagram of reaction click here

Other name(s): SmCPS4

Systematic name: geranylgeranyl-diphosphate hydro-lyase (ent-8α-hydroxylabd-13-en-15-yl diphosphate forming)

Comments: Isolated from the plant Salvia miltiorrhiza (red sage).

References:

1. Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607-1618. [PMID: 26077765]

EC 4.2.1.174

Accepted name: peregrinol diphosphate synthase

Reaction: peregrinol diphosphate = geranylgeranyl diphosphate + H₂O

For diagram of reaction click here

Glossary: peregrinol diphosphate = (13E)-9-hydroxy-8α-labda-13-en-15-yl diphosphate

Other name(s): MvCPS1

Systematic name: geranylgeranyl-diphosphate hydro-lyase (peregrinol diphosphate forming)

Comments: Isolated from the plant Marrubium vulgare (white horehound). Involved in marrubiin biosynthesis.

References:

1. Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914-927. [PMID: 24990389]

EC 4.2.3.157

Accepted name: (+)-isoafricanol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (+)-isoafricanol + diphosphate

For diagram of reaction click here.

Glossary: (+)-isoafricanol = (1aS,4aR,5R,7aS,7bR)-3,3,5,7b-tetramethyldecahydro-4aH-cyclopropa[e]azulen-4a-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-isoafricanol-forming]

Comments: (+)-Isoafricanol is a sesquiterpene alcohol. Its synthesis has been shown to occur in the bacteria Streptomyces violaceusniger and Streptomyces malaysiensis.

References:

1. Riclea, R., Citron, C.A., Rinkel, J. and Dickschat, J.S. Identification of isoafricanol and its terpene cyclase in Streptomyces violaceusniger using CLSA-NMR. Chem. Commun. (Camb.) 50 (2014) 4228-4230. [PMID: 24626486]

2. Rabe, P., Samborskyy, M., Leadlay, P.F. and Dickschat, J.S. Isoafricanol synthase from Streptomyces malaysiensis. Org. Biomol. Chem. 15 (2017) 2353-2358. [PMID: 28247907]

EC 4.2.3.158

Accepted name: (–)-spiroviolene synthase

Reaction: geranylgeranyl diphosphate = (–)-spiroviolene + diphosphate

For diagram of reaction click here and mechanism click here.

Glossary: (–)-spiroviolene = (2R,3a'S,3b'R,5R,6a'R)-2,4',4',5,6a'-pentamethyl-2',3',3a',3b',4',5',6',6a'-octahydrospiro[cyclopentane-1,1'-cyclopenta[a]pentalene]

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase [cyclizing, (–)-spiroviolene-forming]

Comments: The enzyme, which forms the diterpene (–)-spiroviolene, has been characterized from the bacterium Streptomyces violens.

References:

1. Rabe, P., Rinkel, J., Dolja, E., Schmitz, T., Nubbemeyer, B., Luu, T.H. and Dickschat, J.S. Mechanistic investigations of two bacterial diterpene cyclases: spiroviolene synthase and tsukubadiene synthase. Angew. Chem. Int. Ed. Engl. 56 (2017) 2776-2779. [PMID: 28146322]

EC 4.2.3.159

Accepted name: tsukubadiene synthase

Reaction: geranylgeranyl diphosphate = tsukubadiene + diphosphate

For diagram of reaction click here and mechanism click here.

Glossary: tsukubadiene = (1S,3aS,5Z,7aS,10aR,11Z)-1,5,8,8,10a-pentamethyl-2,3,3a,4,7,7a,8,9,10,10a-decahydro-1H-dicyclopenta[a,d][9]annulene

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, tsukubadiene-forming)

Comments: The synthesis of the diterpene tsukubadiene has been shown to occur in the Actinobacterium Streptomyces tsukubaensis.

References:

1. Yamada, Y., Arima, S., Nagamitsu, T., Johmoto, K., Uekusa, H., Eguchi, T., Shin-ya, K., Cane, D.E. and Ikeda, H. Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host. J. Antibiot. (Tokyo) 68 (2015) 385-394. [PMID: 25605043]

2. Rabe, P., Rinkel, J., Dolja, E., Schmitz, T., Nubbemeyer, B., Luu, T.H. and Dickschat, J.S. Mechanistic investigations of two bacterial diterpene cyclases: spiroviolene synthase and tsukubadiene synthase. Angew. Chem. Int. Ed. Engl. 56 (2017) 2776-2779. [PMID: 28146322]

EC 4.2.3.160

Accepted name: (2S,3R,6S,9S)-(–)-protoillud-7-ene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (2S,3R,6S,9S)-(–)-protoillud-7-ene + diphosphate

For diagram of reaction click here and mechanism click here.

Glossary: (2S,3R,6S,9S)-(–)-protoillud-7-ene = (2aS,4aS,7aS,7bR)-3,6,6,7b-tetramethyl-2,2a,4a,5,6,7,7a,7b-octahydro-1H-cyclobuta[e]indene
pentalenene = (3aS,5aS,8aR)-1,4,7,7-tetramethyl-1,2,3,3a,5a,6,7,8-octahydrocyclopenta[c]pentalene

Other name(s): TPS6 (gene name)

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (2S,3R,6S,9S)-(–)-protoillud-7-ene-forming]

Comments: The enzyme has been described from the slime-mould Dictyostelium discoideum. It is specific for (2E,6E)-farnesyl diphosphate. While the major product is the sequiterpene (2S,3R,6S,9S)-(–)-protoillud-7-ene, traces of pentalenene are also formed.

References:

1. Chen, X., Kollner, T.G., Jia, Q., Norris, A., Santhanam, B., Rabe, P., Dickschat, J.S., Shaulsky, G., Gershenzon, J. and Chen, F. Terpene synthase genes in eukaryotes beyond plants and fungi: occurrence in social amoebae. Proc. Natl Acad. Sci. USA 113 (2016) 12132-12137. [PMID: 27790999]

2. Rabe, P., Rinkel, J., Nubbemeyer, B., Kollner, T.G., Chen, F. and Dickschat, J.S. Terpene cyclases from social Amoebae. Angew. Chem. Int. Ed. Engl. 55 (2016) 15420-15423. [PMID: 27862766]

EC 4.2.3.161

Accepted name: (3S)-(+)-asterisca-2(9),6-diene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (3S)-(+)-asterisca-2(9),6-diene + diphosphate

For diagram of reaction click here

Glossary: (3S)-(+)-asterisca-2(9),6-diene = (4S,7Z)-2,2,4,7-tetramethyl-2,3,4,5,6,9-hexahydro-1H-cyclopenta[8]annulene

Other name(s): TPS2 (gene name)

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (3S)-(+)-asterisca-2(9),6-diene-forming]

Comments: The sequiterpene (3S)-(+)-asterisca-2(9),6-diene has been shown to be synthezised in the slime-mould Dictyostelium discoideum. The enzyme is specific for (2E,6E)-farnesyl diphosphate.

References:

1. Chen, X., Kollner, T.G., Jia, Q., Norris, A., Santhanam, B., Rabe, P., Dickschat, J.S., Shaulsky, G., Gershenzon, J. and Chen, F. Terpene synthase genes in eukaryotes beyond plants and fungi: occurrence in social amoebae. Proc. Natl Acad. Sci. USA 113 (2016) 12132-12137. [PMID: 27790999]

2. Rabe, P., Rinkel, J., Nubbemeyer, B., Kollner, T.G., Chen, F. and Dickschat, J.S. Terpene cyclases from social Amoebae. Angew. Chem. Int. Ed. Engl. 55 (2016) 15420-15423. [PMID: 27862766]

EC 4.2.3.162

Accepted name: (–)-α-amorphene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (–)-α-amorphene + diphosphate

For diagram of reaction click here

Glossary: (–)-α-amorphene = (1S,4aR,8aS)-4,7-dimethyl-1-(propan-2-yl)-1,2,4a,5,6,8a-hexahydronaphthalene

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (–)-α-amorphene-forming]

Comments: The enzyme, found in the bacterium Streptomyces viridochromogenes, is specific for (2E,6E)-farnesyl diphosphate and produces only (–)-α-amorphene.

References:

1. Rabe, P. and Dickschat, J.S. Rapid chemical characterization of bacterial terpene synthases. Angew. Chem. Int. Ed. Engl. 52 (2013) 1810-1812. [PMID: 23307484]

2. Rinkel, J., Rabe, P., Garbeva, P. and Dickschat, J.S. Lessons from 1,3-hydride shifts in sesquiterpene cyclizations. Angew. Chem. Int. Ed. Engl. 55 (2016) 13593-13596. [PMID: 27666571]

3. Rabe, P., Schmitz, T. and Dickschat, J.S. Mechanistic investigations on six bacterial terpene cyclases. Beilstein J. Org. Chem. 12 (2016) 1839-1850. [PMID: 27829890]

EC 4.2.3.163

Accepted name: (+)-corvol ether B synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (+)-corvol ether B + diphosphate

For diagram of reaction click here

Glossary: (+)-corvol ether B = (1S,3R,5aR,6S,8aR)-3,6-dimethyl-1-(propan-2-yl)hexahydro-1H,3H-3,8a-methanocyclopenta[c]oxepine

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-corvol ether B-forming]

Comments: The enzyme, which forms the sesquiterpene (+)-corvol ether B, has been reported from the bacterium Kitasatospora setae.

References:

1. Rabe, P., Pahirulzaman, K.A. and Dickschat, J.S. Structures and biosynthesis of corvol ethers —sesquiterpenes from the actinomycete Kitasatospora setae. Angew. Chem. Int. Ed. Engl. 54 (2015) 6041-6045. [PMID: 25809275]

2. Rabe, P., Janusko, A., Goldfuss, B. and Dickschat, J.S. Experimental and theoretical studies on corvol ether biosynthesis. Chembiochem. 17 (2016) 146-149. [PMID: 26635093]

3. Rinkel, J., Rabe, P., Garbeva, P. and Dickschat, J.S. Lessons from 1,3-hydride shifts in sesquiterpene cyclizations. Angew. Chem. Int. Ed. Engl. 55 (2016) 13593-13596. [PMID: 27666571]

EC 4.2.3.164

Accepted name: (+)-eremophilene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-eremophilene + diphosphate

For diagram of reaction click here

Glossary: (+)-eremophilene = (3S,4aS,5R)-4a,5-dimethyl-3-(prop-1-en-2-yl)-1,2,3,4,4a,5,6,7-octahydronaphthalene

Other name(s): STC3 (gene name); geoA (gene name)

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-eremophilene-forming]

Comments: The enzyme has been identified in the myxobacterium Sorangium cellulosum and in the fungus Fusarium fujikuroi.

References:

1. Schifrin, A., Ly, T.T., Gunnewich, N., Zapp, J., Thiel, V., Schulz, S., Hannemann, F., Khatri, Y. and Bernhardt, R. Characterization of the gene cluster CYP264B1-geoA from Sorangium cellulosum So ce56: biosynthesis of (+)-eremophilene and its hydroxylation. Chembiochem 16 (2015) 337-344. [PMID: 25504914]

2. Burkhardt, I., Siemon, T., Henrot, M., Studt, L., Rosler, S., Tudzynski, B., Christmann, M. and Dickschat, J.S. Mechanistic characterisation of two sesquiterpene cyclases from the plant pathogenic fungus Fusarium fujikuroi. Angew. Chem. Int. Ed. Engl. 55 (2016) 8748-8751. [PMID: 27294564]

EC 4.2.3.165

Accepted name: (1R,4R,5S)-(–)-guaia-6,10(14)-diene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (1R,4R,5S)-(–)-guaia-6,10(14)-diene + diphosphate

For diagram of reaction click here

Glossary: (1R,4R,5S)-(–)-guaia-6,10(14)-diene = (1R)-1-methyl-4-methylidene-7-(propan-2-yl)-1,2,3,3a,4,5,6,8a-octahydroazulene = (1R)-7-isopropyl-1-methyl-4-methylene-1,2,3,3a,4,5,6,8a-octahydroazulene

Other name(s): STC5 (gene name)

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (1R,4R,5S)-(–)-guaia-6,10(14)-diene-forming]

Comments: The original enzyme (STC5) from the fungus Fusarium fujikuroi is inactive because of a critically naturally occuring mutation that leads to an asparagine to lysine exchange in the NSE (Asn-Ser-Glu) triad, a highly conserved motif of type I terpene cyclases. Sequence correction by site-directed mutagenesis (K288N) restores activity.

References:

1. Burkhardt, I., Siemon, T., Henrot, M., Studt, L., Rosler, S., Tudzynski, B., Christmann, M. and Dickschat, J.S. Mechanistic characterisation of two sesquiterpene cyclases from the plant pathogenic fungus Fusarium fujikuroi. Angew. Chem. Int. Ed. Engl. 55 (2016) 8748-8751. [PMID: 27294564]

EC 4.2.3.166

Accepted name: (+)-(1E,4E,6S,7R)-germacra-1(10),4-dien-6-ol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (+)-(1E,4E,6S,7R)-germacra-1(10),4-dien-6-ol + diphosphate

For diagram of reaction click here

Glossary: (+)-(1E,4E,6S,7R)-germacra-1(10),4-dien-6-ol = (1S,2E,6E,10R)-3,7-dimethyl-10-(propan-2-yl)cyclodeca-2,6-dien-1-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-(1E,4E,6S,7R)-germacra-1(10),4-dien-6-ol-forming]

Comments: The enzyme has been identified in the bacterium Streptomyces pratensis. It is specific for (2E,6E)-farnesyl diphosphate.

References:

1. Rabe, P., Barra, L., Rinkel, J., Riclea, R., Citron, C.A., Klapschinski, T.A., Janusko, A. and Dickschat, J.S. Conformational analysis, thermal rearrangement, and EI-MS fragmentation mechanism of ((1(10)E,4E,6S,7R)-germacradien-6-ol by ¹³C-labeling experiments. Angew. Chem. Int. Ed. Engl. 54 (2015) 13448-13451. [PMID: 26361082]

EC 4.2.3.167

Accepted name: dolabella-3,7-dien-18-ol synthase

Reaction: geranylgeranyl diphosphate + H₂O = (3E,7E)-dolabella-3,7-dien-18-ol + diphosphate

For diagram of reaction click here

Glossary: (3E,7E)-dolabella-3,7-dien-18-ol = 2-[(1R,3aR,5E,9E,12aR)-3a,6,10-trimethyl-1,2,3,3a,4,7,8,11,12,12a-decahydrocyclopenta[11]annulen-1-yl]propan-2-ol

Other name(s): TPS20 (gene name)

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase [cyclizing, (3E,7E)-dolabella-3,7-dien-18-ol-forming]

Comments: Isolated from an ecotype of the plant Arabidopsis thaliana from Cape Verde Islands. The enzyme also gives (3E,7E)-dolathalia-3,7,11-triene and traces of other terpenoids. cf. EC 4.2.3.168 dolathalia-3,7,11-triene synthase.

References:

1. Wang, Q., Jia, M., Huh, J.H., Muchlinski, A., Peters, R.J. and Tholl, D. Identification of a dolabellane type diterpene synthase and other root-expressed diterpene synthases in Arabidopsis. Front. Plant Sci. 7 (2016) 1761. [PMID: 27933080]

EC 4.2.3.168

Accepted name: dolathalia-3,7,11-triene synthase

Reaction: geranylgeranyl diphosphate = (3E,7E)-dolathalia-3,7,11-triene + diphosphate

For diagram of reaction click here

Glossary: (3E,7E)-dolathalia-3,7,11-triene = (7E,11E)-3,3,7,11,13a-pentamethy1-2,3,5,6,9,10,13,13a-octahydro-1H-benzo[11]annulene

Other name(s): TPS20 (gene name)

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase [cyclizing, (3E,7E)-dolathalia-3,7,11-triene-forming]

Comments: Isolated from an ecotype of the plant Arabidopsis thaliana from Cape Verde Islands. The enzyme also gives (3E,7E)-dolabella-3,7-dien-18-ol and traces of other terpenoids. cf. EC 4.2.3.167 dolabella-3,7-dien-18-ol synthase.

References:

1. Wang, Q., Jia, M., Huh, J.H., Muchlinski, A., Peters, R.J. and Tholl, D. Identification of a dolabellane type diterpene synthase and other root-expressed diterpene synthases in Arabidopsis. Front. Plant Sci. 7 (2016) 1761. [PMID: 27933080]

EC 4.2.3.169

Accepted name: 7-epi-α-eudesmol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = 7-epi-α-eudesmol + diphosphate

For diagram of reaction click here

Glossary: 7-epi-α-eudesmol = 2-[(2S,4aR,8aR)-4a,8-dimethyl-1,2,3,4,4a,5,6,8a-octahydronaphthalen-2-yl]propan-2-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 7-epi-α-eudesmol-forming)

Comments: The enzyme, found in the bacterium Streptomyces viridochromogenes, is specific for (2E,6E)-farnesyl diphosphate.

References:

1. Rabe, P., Schmitz, T. and Dickschat, J.S. Mechanistic investigations on six bacterial terpene cyclases. Beilstein J. Org. Chem. 12 (2016) 1839-1850. [PMID: 27829890]

EC 4.2.3.170

Accepted name: 4-epi-cubebol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = 4-epi-cubebol + diphosphate

For diagram of reaction click here

Glossary: 4-epi-cubebol = (3S,3aS,3bR,4S,7S,7aS)-4-(2-hydroxypropan-2-yl)-7-methyloctahydro-1H-cyclopenta[1,3]cyclopropa[1,2]benzen-3-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 4-epi-cubebol-forming)

Comments: The enzyme, found in the bacterium Streptosporangium roseum, is specific for (2E,6E)-farnesyl diphosphate.

References:

1. Rabe, P., Schmitz, T. and Dickschat, J.S. Mechanistic investigations on six bacterial terpene cyclases. Beilstein J. Org. Chem. 12 (2016) 1839-1850. [PMID: 27829890]

EC 4.2.3.171

Accepted name: (+)-corvol ether A synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (+)-corvol ether A + diphosphate

For diagram of reaction click here

Glossary: (+)-corvol ether A = (1R,4S,4aR,7R,8aR)-4,7-dimethyl-1-(propan-2-yl)decahydro-1,7-epoxynaphthalene

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-corvol ether A-forming]

Comments: The enzyme, which forms the sesquiterpene (+)-corvol ether A, has been reported from the bacterium Kitasatospora setae.

References:

1. Rabe, P., Pahirulzaman, K.A. and Dickschat, J.S. Structures and biosynthesis of corvol ethers —sesquiterpenes from the actinomycete Kitasatospora setae. Angew. Chem. Int. Ed. Engl. 54 (2015) 6041-6045. [PMID: 25809275]

2. Rabe, P., Janusko, A., Goldfuss, B. and Dickschat, J.S. Experimental and theoretical studies on corvol ether biosynthesis. Chembiochem. 17 (2016) 146-149. [PMID: 26635093]

3. Rinkel, J., Rabe, P., Garbeva, P. and Dickschat, J.S. Lessons from 1,3-hydride shifts in sesquiterpene cyclizations. Angew. Chem. Int. Ed. Engl. 55 (2016) 13593-13596. [PMID: 27666571]

EC 4.2.3.172

Accepted name: 10-epi-juneol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = 10-epi-juneol + diphosphate

For diagram of reaction click here

Glossary: 10-epi-juneol = 10α-eudesm-4(14)-en-6α-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 10-epi-juneol-forming)

Comments: Isolated from the plant Inula hupehensis. The enzyme also gives gives τ-cadinol and traces of other terpenoids, see EC 4.2.3.173, τ-cadinol synthase.

References:

1. Gou, J.B., Li, Z.Q., Li, C.F., Chen, F.F., Lv, S.Y. and Zhang, Y.S. Molecular cloning and functional analysis of a 10-epi-junenol synthase from Inula hupehensis. Plant Physiol. Biochem. 106 (2016) 288-294. [PMID: 27231873]

EC 4.2.3.173

Accepted name: τ-cadinol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = τ-cadinol + diphosphate

For diagram of reaction click here

Glossary: τ-cadinol = 10β-cadin-4-en-10-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, τ-cadinol-forming)

Comments: Isolated from the plant Inula hupehensis. The enzyme also gives 10-epi-juneol and traces of other terpenoids, see EC 4.2.3.172, 10-epi-juneol synthase. It has also been isolated from the plants maize (Zea mays) and lavender (Lavandula angustifolia).

References:

1. Gou, J.B., Li, Z.Q., Li, C.F., Chen, F.F., Lv, S.Y. and Zhang, Y.S. Molecular cloning and functional analysis of a 10-epi-junenol synthase from Inula hupehensis. Plant Physiol. Biochem. 106 (2016) 288-294. [PMID: 27231873]

2. Jullien, F., Moja, S., Bony, A., Legrand, S., Petit, C., Benabdelkader, T., Poirot, K., Fiorucci, S., Guitton, Y., Nicole, F., Baudino, S. and Magnard, J.L. Isolation and functional characterization of a τ-cadinol synthase, a new sesquiterpene synthase from Lavandula angustifolia. Plant Mol. Biol. 84 (2014) 227-241. [PMID: 24078339]

3. Ren, F., Mao, H., Liang, J., Liu, J., Shu, K. and Wang, Q. Functional characterization of ZmTPS7 reveals a maize τ-cadinol synthase involved in stress response. Planta 244 (2016) 1065-1074. [PMID: 27421723]

EC 4.2.3.174

Accepted name: (2E,6E)-hedycaryol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (2E,6E)-hedycaryol + diphosphate

For diagram of reaction click here

Glossary: (2E,6E)-hedycaryol = (1E,4E,7S)-germacra-1(10),4-dien-11-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (2E,6E)-hedycaryol-forming]

Comments: Isolated from the plant Camellia brevistyla. See also EC 4.2.3.187, (2Z,2E)-hedycaryol synthase.

References:

1. Hattan, J., Shindo, K., Ito, T., Shibuya, Y., Watanabe, A., Tagaki, C., Ohno, F., Sasaki, T., Ishii, J., Kondo, A. and Misawa, N. Identification of a novel hedycaryol synthase gene isolated from Camellia brevistyla flowers and floral scent of Camellia cultivars. Planta 243 (2016) 959-972. [PMID: 26744017]

EC 4.2.3.175

Accepted name: 10-epi-cubebol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = 10-epi-cubebol + diphosphate

For diagram of reaction click here

Other name(s): sce6369

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 10-epi-cubebol-forming)

Comments: Isolated from the bacterium Sorangium cellulosum So ce56. The enzyme is also responsible for the formation of trace amounts of many other sesquiterpenes, mainly cadinanes and cubebanes.

References:

1. Schifrin, A., Khatri, Y., Kirsch, P., Thiel, V., Schulz, S. and Bernhardt, R. A single terpene synthase is responsible for a wide variety of sesquiterpenes in Sorangium cellulosum Soce56. Org. Biomol. Chem. 14 (2016) 3385-3393. [PMID: 26947062]

EC 4.2.3.176

Accepted name: sesterfisherol synthase

Reaction: (2E,6E,10E,14E)-geranylfarnesyl diphosphate + H₂O = sesterfisherol + diphosphate

For diagram of reaction click here Glossary: sesterfisherol = (3R,3aS,6S,6aR,7aR,10R,10aS,11aR)-3,6,7a,12-tetramethyl-10-(propan-2-yl)-2,3,3a,4,5,6,6a,7,7a,8,9,10,10a,11-tetradecahydrocyclopenta[4,5]cycloocta[f]inden-11a(1H)-ol

Other name(s): NfSS

Systematic name: (2E,6E,10E,14E)-geranylfarnesyl-diphosphate diphosphate-lyase (cyclizing, sesterfisherol-forming)

Comments: Isolated from the fungus Neosartorya fischeri.

References:

1. Ye, Y., Minami, A., Mandi, A., Liu, C., Taniguchi, T., Kuzuyama, T., Monde, K., Gomi, K. and Oikawa, H. Genome mining for sesterterpenes using bifunctional terpene synthases reveals a unified intermediate of di/sesterterpenes. J. Am. Chem. Soc. 137 (2015) 11846-11853. [PMID: 26332841]

EC 4.2.3.177

Accepted name: β-thujene synthase

Reaction: geranyl diphosphate = β-thujene + diphosphate

For diagram of reaction click here

Other name(s): CoTPS1

Systematic name: geranyl-diphosphate diphosphate-lyase (cyclizing, β-thujene-forming)

Comments: Isolated from the plant Cananga odorata var. fruticosa (ylang ylang). The enzyme forms roughly equal proportions of β-thujene, sabinene, β-pinene and α-terpinene see EC 4.2.3.109/EC 4.2.3.110 sabinene synthase, EC 4.2.3.120/EC 4.2.3.122 β-pinene synthase, EC 4.2.3.115 α-terpinene synthase.

References:

1. Jin, J., Kim, M.J., Dhandapani, S., Tjhang, J.G., Yin, J.L., Wong, L., Sarojam, R., Chua, N.H. and Jang, I.C. The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa) uncovers biosynthetic pathways for volatile organic compounds and a multifunctional and novel sesquiterpene synthase. J. Exp. Bot. 66 (2015) 3959-3975. [PMID: 25956881]

EC 4.2.3.178

Accepted name: stellata-2,6,19-triene synthase

Reaction: (2E,6E,10E,14E)-geranylfarnesyl diphosphate = stellata-2,6,19-triene + diphosphate

For diagram of reaction click here Glossary: stellata-2,6,19-triene = (3S,3aR,5aR,7E,11E,14aR,14bR)-5a,8,12,14b-tetramethyl-3-(prop-1-en-2-yl)-1,2,3,3a,4,5,5a,6,9,10,13,14,14a,14b-tetradecahydrocycloundeca[e]indene

Systematic name: (2E,6E,10E,14E)-geranylfarnesyl-diphosphate diphosphate-lyase (cylizing, stellata-2,6,19-triene-forming)

Comments: Isolated from the fungus Aspergillus stellatus.

References:

1. Matsuda, Y., Mitsuhashi, T., Quan, Z. and Abe, I. Molecular basis for stellatic acid biosynthesis: a genome mining approach for discovery of sesterterpene synthases. Org. Lett. 17 (2015) 4644-4647. [PMID: 26351860]

EC 4.2.3.179

Accepted name: guaia-4,6-diene synthase

Reaction: (2E,6E)-farnesyl diphosphate = guaia-4,6-diene + diphosphate

For diagram of reaction click here

Other name(s): XsTPS2

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, guaia-4,6-diene-forming)

Comments: Isolated from the plant Xanthium strumarium (rough cocklebur).

References:

1. Li, Y., Chen, F., Li, Z., Li, C. and Zhang, Y. Identification and functional characterization of sesquiterpene synthases from Xanthium strumarium. Plant Cell Physiol 57 (2016) 630-641. [PMID: 26858282]

EC 4.2.3.180

Accepted name: pseudolaratriene synthase

Reaction: geranylgeranyl diphosphate = pseudolaratriene + diphosphate

For diagram of reaction click here

Glossary: pseudolaradiene = (1RS,3aSR,8aRS)-3a,6-dimethyl-1-(6-methylhepta-2,5-dien-2-yl)-1,2,3,3a,4,7,8,8a-octahydrohydroazulene

Other name(s): PxaTPS8

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, pseudolaradiene-forming)

Comments: Isolated from the plant Pseudolarix amabilis (golden larch). The product is oxidized to pseudolaric acid B, a microtubule-destabilizing agent.

References:

1. Mafu, S., Karunanithi, P.S., Palazzo, T.A., Harrod, B.L., Rodriguez, S.M., Mollhoff, I.N., O'Brien, T.E., Tong, S., Fiehn, O., Tantillo, D.J., Bohlmann, J. and Zerbe, P. Biosynthesis of the microtubule-destabilizing diterpene pseudolaric acid B from golden larch involves an unusual diterpene synthase. Proc. Natl Acad. Sci. USA 114 (2017) 974-979. [PMID: 28096378]

EC 4.2.3.181

Accepted name: selina-4(15),7(11)-diene synthase

Reaction: (2E,6E)-farnesyl diphosphate = selina-4(15),7(11)-diene + diphosphate

For diagram of reaction click here

Other name(s): SdS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, selina-4(15),7(11)-diene-forming)

Comments: Isolated from the bacteria Streptomyces pristinaespiralis and S. somaliensis.

References:

1. Rabe, P. and Dickschat, J.S. Rapid chemical characterization of bacterial terpene synthases. Angew. Chem. Int. Ed. Engl. 52 (2013) 1810-1812. [PMID: 23307484]

2. Baer, P., Rabe, P., Fischer, K., Citron, C.A., Klapschinski, T.A., Groll, M. and Dickschat, J.S. Induced-fit mechanism in class I terpene cyclases. Angew. Chem. Int. Ed. Engl. 53 (2014) 7652-7656. [PMID: 24890698]

EC 4.2.3.182

Accepted name: pristinol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (+)-(2S,3R,9R)-pristinol + diphosphate

For diagram of reaction click here and mechanism click here.

Glossary: (+)-(2S,3R,9R)-pristinol = (1R,6R,9aS)-1,4,8,8-tetramethyl-2,3,5,6,7,8,9,9a-octahydro-1H-cyclopenta[8]annulen-6-ol

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-(2S,3R,9R)-pristinol-forming]

Comments: Isolated from the bacterium Streptomyces pristinaespiralis.

References:

1. Klapschinski, T.A., Rabe, P. and Dickschat, J.S. Pristinol, a sesquiterpene alcohol with an unusual skeleton from Streptomyces pristinaespiralis. Angew. Chem. Int. Ed. Engl. 55 (2016) 10141-10144. [PMID: 27403888]

EC 4.2.3.183

Accepted name: nezukol synthase

Reaction: (+)-copalyl diphosphate + H₂O = nezukol + diphosphate

For diagram of reaction click here

Glossary: (+)-copalyl diphosphate = (2E)-3-methyl-5-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate
nezukol = pimar-15-en-8-ol

Other name(s): TPS2

Systematic name: (+)-copalyl-diphosphate diphosphate-lyase (cyclizing, nezukol-forming)

Comments: Isolated from the plant Isodon rubescens.

References:

1. Pelot, K.A., Hagelthorn, D.M., Addison, J.B. and Zerbe, P. Biosynthesis of the oxygenated diterpene nezukol in the medicinal plant Isodon rubescens is catalyzed by a pair of diterpene synthases. PLoS One 12 (2017) e0176507. [PMID: 28445526]

EC 4.2.3.184

Accepted name: 5-hydroxy-α-gurjunene synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = 5-hydroxy-α-gurjunene + diphosphate

For diagram of reaction click here

Other name(s): MpMTPSL4

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 5-hydroxy-α-gurjunene-forming)

Comments: Isolated from the liverwort Marchantia polymorpha.

References:

1. Kumar, S., Kempinski, C., Zhuang, X., Norris, A., Mafu, S., Zi, J., Bell, S.A., Nybo, S.E., Kinison, S.E., Jiang, Z., Goklany, S., Linscott, K.B., Chen, X., Jia, Q., Brown, S.D., Bowman, J.L., Babbitt, P.C., Peters, R.J., Chen, F. and Chappell, J. Molecular diversity of terpene synthases in the liverwort Marchantia polymorpha. Plant Cell 28 (2016) 2632-2650. [PMID: 27650333]

EC 4.2.3.185

Accepted name: ent-atiserene synthase

Reaction: ent-copalyl diphosphate = ent-atiserene + diphosphate

For diagram of reaction click here and mechanism click here

Other name(s): IrKSL4

Systematic name: ent-copalyl-diphosphate diphosphate-lyase (cyclizing, ent-atiserine-forming)

Comments: Isolated from the plant Isodon rubescens.

References:

1. Jin, B., Cui, G., Guo, J., Tang, J., Duan, L., Lin, H., Shen, Y., Chen, T., Zhang, H. and Huang, L. Functional diversification of kaurene synthase-like genes in Isodon rubescens. Plant Physiol. 174 (2017) 943-955. [PMID: 28381502]

EC 4.2.3.186

Accepted name: ent-13-epi-manoyl oxide synthase

Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = ent-13-epi-manoyl oxide + diphosphate

For diagram of reaction click here

Glossary: Ent-13-epi-manoyl oxide = (13R)-ent-8,13-epoxylabd-14-ene

Other name(s): SmKSL2; ent-LDPP synthase

Systematic name: ent-8α-hydroxylabd-13-en-15-yl-diphosphate diphosphate-lyase (cyclizing, ent-13-epi-manoyl-oxide-forming)

Comments: Isolated from the plant Salvia miltiorrhiza (red sage).

References:

1. Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607-1618. [PMID: 26077765]

EC 4.2.3.187

Accepted name: (2Z,6E)-hedycaryol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (2Z,6E)-hedycaryol + diphosphate

For diagram of reaction click here

Glossary: (2Z,6E)-hedycaryol = (1E,4Z,7S)-germacra-1(10),4-dien-11-ol

Other name(s): HcS

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (2Z,6E)-hedycaryol-forming]

Comments: Isolated from the bacterium Kitasatospora setae. The stereochemistry suggests the farnesyl diphosphate rearranges to nerolidyl diphosphate or an equivalent intermediate before cyclization. See also EC 4.2.3.174 (2E,6E)-hedycaryol synthase.

References:

1. Baer, P., Rabe, P., Citron, C.A., de Oliveira Mann, C.C., Kaufmann, N., Groll, M. and Dickschat, J.S. Hedycaryol synthase in complex with nerolidol reveals terpene cyclase mechanism. Chembiochem 15 (2014) 213-216. [PMID: 24399794]

EC 4.2.3.188

Accepted name: β-geranylfarnesene synthase

Reaction: (1) all-trans-geranylfarnesyl diphosphate = β-geranylfarnesene + diphosphate
(2) all-trans-hexaprenyl diphosphate = β-hexaprene + diphosphate
(3) all-trans-heptaprenyl diphosphate = β-heptaprene + diphosphate

For diagram of reaction click here or click here.

Glossary: β-geranylfarnesene = (6E,10E,14E)-7,11,15,19-tetramethyl-3-methyleneicosa-1,6,10,14,18-pentaene

Other name(s): Bcl-TS

Systematic name: all-trans-geranylfarnesyl-diphosphate diphosphate-lyase (β-geranylfarnesene-forming)

Comments: Isolated from the bacterium Bacillus clausii. The enzyme acts on a range of polyprenyl diphosphates.

References:

1. Sato, T., Yamaga, H., Kashima, S., Murata, Y., Shinada, T., Nakano, C. and Hoshino, T. Identification of novel sesterterpene/triterpene synthase from Bacillus clausii. Chembiochem 14 (2013) 822-825. [PMID: 23554321]

2. Ueda, D., Yamaga, H., Murakami, M., Totsuka, Y., Shinada, T. and Sato, T. Biosynthesis of sesterterpenes, head-to-tail triterpenes, and sesquarterpenes in Bacillus clausii: identification of multifunctional enzymes and analysis of isoprenoid metabolites. Chembiochem 16 (2015) 1371-1377. [PMID: 25882275]

EC 4.2.3.189

Accepted name: 9,13-epoxylabda-14-ene synthase

Reaction: peregrinol diphosphate = (13ξ)-9,13-epoxylabda-14-ene + diphosphate

For diagram of reaction click here

Glossary: peregrinol diphosphate = (13E)-9-hydroxy-8α-labda-13-en-15-yl diphosphate

Other name(s): MvELS

Systematic name: peregrinol-diphosphate diphosphate-lyase (9,13-epoxylabda-14-ene-forming)

Comments: Isolated from the plant Marrubium vulgare (white horehound). Involved in marrubiin biosynthesis.

References:

1. Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914-927. [PMID: 24990389]

EC 4.2.3.190

Accepted name: manoyl oxide synthase

Reaction: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = manoyl oxide + diphosphate

For diagram of reaction click here

Glossary: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = 8-hydroxycopalyl diphosphate
manoyl oxide = (13R)-8,13-epoxylabd-14-ene

Other name(s): GrTPS6; CfTPS3; CfTPS4; MvELS

Systematic name: (13E)-8α-hydroxylabd-13-en-15-yl-diphosphate diphosphate-lyase (manoyl-oxide-forming)

Comments: Manoyl oxide is found in many plants. This enzyme has been isolated from the plants, Grindelia hirsutula (gum weed), Plectranthus barbatus (forskohlii) and Marrubium vulgare (white horehound).

References:

1. Zerbe, P., Hamberger, B., Yuen, M.M., Chiang, A., Sandhu, H.K., Madilao, L.L., Nguyen, A., Hamberger, B., Bach, S.S. and Bohlmann, J. Gene discovery of modular diterpene metabolism in nonmodel systems. Plant Physiol. 162 (2013) 1073-1091. [PMID: 23613273]

2. Pateraki, I., Andersen-Ranberg, J., Hamberger, B., Heskes, A.M., Martens, H.J., Zerbe, P., Bach, S.S., Moller, B.L., Bohlmann, J. and Hamberger, B. Manoyl oxide (13R), the biosynthetic precursor of forskolin, is synthesized in specialized root cork cells in Coleus forskohlii. Plant Physiol. 164 (2014) 1222-1236. [PMID: 24481136]

3. Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914-927. [PMID: 24990389]

EC 4.2.3.191

Accepted name: cycloaraneosene synthase

Reaction: geranylgeranyl diphosphate = cycloaraneosene + diphosphate

For diagram of reaction click here

Glossary: cycloaraneosene = (1R,3aR,9aS,10aR)-1,9a-dimethyl-4-methylene-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a,10,10a-dodecahydrodicyclopenta[a,d][8]annulene

Other name(s): SdnA

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cycloaraneosene-forming)

Comments: Isolated from the fungus Sordaria araneosa. Cycloaraneosene is a precursor of the antibiotic sordarin.

References:

1. Kudo, F., Matsuura, Y., Hayashi, T., Fukushima, M. and Eguchi, T. Genome mining of the sordarin biosynthetic gene cluster from Sordaria araneosa Cain ATCC 36386: characterization of cycloaraneosene synthase and GDP-6-deoxyaltrose transferase. J. Antibiot. (Tokyo) 69 (2016) 541-548. [PMID: 27072286]

EC 4.2.3.192

Accepted name: labda-7,13(16),14-triene synthase

Reaction: (13E)-labda-7,13-dienyl diphosphate = labda-7,13(16),14-triene + diphosphate

For diagram of reaction click here

Other name(s): SCLAV_p0491

Systematic name: (13E)-labda-7,13-dienyl-diphosphate diphosphate-lyase (labda-7,13(16),14-triene-forming)

Comments: Isolated from the bacterium Streptomyces clavuligerus.

References:

1. Yamada, Y., Komatsu, M. and Ikeda, H. Chemical diversity of labdane-type bicyclic diterpene biosynthesis in Actinomycetales microorganisms. J. Antibiot. (Tokyo) 69 (2016) 515-523. [PMID: 26814669]

EC 4.2.3.193

Accepted name: (12E)-labda-8(17),12,14-triene synthase

Reaction: (+)-copalyl diphosphate = (12E)-labda-8(17),12,14-triene + diphosphate

For diagram of reaction click here

Other name(s): CldD

Systematic name: (+)-copalyl-diphosphate diphosphate-lyase [(12E)-labda-8(17),12,14-triene-forming]

Comments: Isolated from the bacterium Streptomyces cyslabdanicus.

References:

1. Yamada, Y., Komatsu, M. and Ikeda, H. Chemical diversity of labdane-type bicyclic diterpene biosynthesis in Actinomycetales microorganisms. J. Antibiot. (Tokyo) 69 (2016) 515-523. [PMID: 26814669]

EC 4.2.3.194

Accepted name: (–)-drimenol synthase

Reaction: (2E,6E)-farnesyl diphosphate + H₂O = (–)-drimenol + diphosphate

For diagram of sesquiterpenoid biosynthesis, click here

Glossary: (–)-drimenol = drim-7-en-11-ol

Other name(s): PhDS; VoTPS3; farnesyl pyrophosphate:drimenol cyclase; drimenol cyclase; (2E,6E)-farnesyl-diphosphate diphosphohydrolase (drimenol-forming)

Systematic name: (2E,6E)-farnesyl-diphosphate diphospho-lyase [cyclising, (–)-drimenol-forming]

Comments: Isolated from the plants Valeriana officinalis (valerian) and Persicaria hydropiper (water pepper). The enzyme does not act on farnesol or drimenol diphosphate. Using 18-oxygen labelled water 18-oxygen was incorporated suggesting involvement of a stabilised carbocation or an equivalent species.

References:

1. Banthorp, D.V., Brown, J.T. and Morris, G.S. Partial purification of farnesyl pyrophosphate:drimenol cyclase and geranylgerany pyrophosphate:sclareol cyclase, using cell culture as a source of material. Phytochemistry 31 (1992) 3391-3395.

2. Kwon, M., Cochrane, S.A., Vederas, J.C. and Ro, D.K. Molecular cloning and characterization of drimenol synthase from valerian plant (Valeriana officinalis). FEBS Lett. 588 (2014) 4597-4603. [PMID: 25447532]

3. Henquet, M.GL., Prota, N., van der Hooft, J.JJ., Varbanova-Herde, M., Hulzink, R.JM., de Vos, M., Prins, M., de Both, M.TJ., Franssen, M.CR., Bouwmeester, H. and Jongsma, M. Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes. Plant J. 90 (2017) 1052-1063. [PMID: 28258968]

EC 4.3.2.7

Accepted name: glutathione-specific γ-glutamylcyclotransferase

Reaction: glutathione = L-cysteinylglycine + 5-oxo-L-proline

For diagram of reaction click here and mechanism click here

Other name(s): γ-GCG; CHAC (gene name); CHAC1 (gene name); CHAC2 (gene name)

Systematic name: glutathione γ-glutamyl cyclotransferase (5-oxo-L-proline producing)

Comments: The enzyme, found in bacteria, fungi and animals, is specific for glutathione (cf. EC 4.3.2.9, γ-glutamylcyclotransferase). The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the L-glutamyl residue, releasing it as the cyclic 5-oxo-L-proline.

References:

1. Kumar, A., Tikoo, S., Maity, S., Sengupta, S., Sengupta, S., Kaur, A. and Bachhawat, A.K. Mammalian proapoptotic factor ChaC1 and its homologues function as γ-glutamyl cyclotransferases acting specifically on glutathione. EMBO Rep. 13 (2012) 1095-1101. [PMID: 23070364]

2. Kaur, A., Gautam, R., Srivastava, R., Chandel, A., Kumar, A., Karthikeyan, S. and Bachhawat, A.K. ChaC₂, an enzyme for slow turnover of cytosolic glutathione. J. Biol. Chem. 292 (2017) 638-651. [PMID: 27913623]

EC 4.3.2.8

Accepted name: γ-glutamylamine cyclotransferase

Reaction: ε-(γ-L-glutamyl)-L-lysine = L-lysine + 5-oxo-L-proline

Other name(s): GGACT

Systematic name: ε-(γ-L-glutamyl)-L-lysine γ-glutamyl cyclotransferase (5-oxo-L-proline producing)

Comments: The enzyme, found in vertebrates, has no activity toward α-(γ-L-glutamyl)-L-amino acids (cf. EC 4.3.2.9, γ-glutamylcyclotransferase). The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the γ-L-glutamyl residue, releasing it as the cyclic 5-oxo-L-proline.

References:

1. Fink, M.L., Chung, S.I. and Folk, J.E. γ-Glutamylamine cyclotransferase: specificity toward ε-(L-γ-glutamyl)-L-lysine and related compounds. Proc. Natl Acad. Sci. USA 77 (1980) 4564-4568. [PMID: 6107907]

2. Oakley, A.J., Coggan, M. and Board, P.G. Identification and characterization of γ-glutamylamine cyclotransferase, an enzyme responsible for γ-glutamyl-ε-lysine catabolism. J. Biol. Chem. 285 (2010) 9642-9648. [PMID: 20110353]

EC 4.3.2.9

Accepted name: γ-glutamylcyclotransferase

Reaction: α-(γ-L-glutamyl)-L-amino acid = α-L-amino acid + 5-oxo-L-proline

Other name(s): γ-glutamyl-amino acid cyclotransferase; γ-L-glutamylcyclotransferase; L-glutamic cyclase; (5-L-glutamyl)-L-amino-acid 5-glutamyltransferase (cyclizing); GGCT

Systematic name: α-(γ-L-glutamyl)-L-amino-acid γ-glutamyl cyclotransferase (5-oxo-L-proline producing)

Comments: The enzyme, found in animals and plants, acts on derivatives of L-glutamate, L-2-aminobutanoate, L-alanine and glycine. The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the L-glutamyl residue, releasing it as the cyclic 5-oxo-L-proline.

References:

1. Bodnaryk, R.P. and McGirr, L. Purification, properties and function of a unique γ-glutamyl cyclotransferase from the housefly, Musca domestica L. Biochim. Biophys. Acta 315 (1973) 352-362.

2. Orlowski, M., Richman, P.G. and Meister, A. Isolation and properties of γ-L-glutamylcyclotransferase from human brain. Biochemistry 8 (1969) 1048-1055. [PMID: 5781001]

3. Oakley, A.J., Yamada, T., Liu, D., Coggan, M., Clark, A.G. and Board, P.G. The identification and structural characterization of C7orf24 as γ-glutamyl cyclotransferase. An essential enzyme in the γ-glutamyl cycle. J. Biol. Chem. 283 (2008) 22031-22042. [PMID: 18515354]

4. Paulose, B., Chhikara, S., Coomey, J., Jung, H.I., Vatamaniuk, O. and Dhankher, O.P. A γ-glutamyl cyclotransferase protects Arabidopsis plants from heavy metal toxicity by recycling glutamate to maintain glutathione homeostasis. Plant Cell 25 (2013) 4580-4595. [PMID: 24214398]

EC 4.4.1.36

Accepted name: hercynylcysteine S-oxide lyase

Reaction: S-(hercyn-2-yl)-L-cysteine S-oxide + reduced acceptor = ergothioneine + pyruvate + ammonia + acceptor (overall reaction)
(1a) S-(hercyn-2-yl)-L-cysteine S-oxide + H₂O = 2-(hydroxysulfanyl)hercynine + pyruvate + ammonia
(1b) 2-(hydroxysulfanyl)hercynine + reduced acceptor = ergothioneine + acceptor + H₂O (spontaneous)

Glossary: 2-(hydroxysulfanyl)hercynine = N^α,N^α,N^α-trimethyl-2-(hydroxysulfanyl)-L-histidine = 2-sulfenohercynine
ergothioneine = N^α,N^α,N^α-trimethyl-2-sulfanylidene-2,3-dihydro-L-histidine

Other name(s): egtE (gene name)

Systematic name: S-(hercyn-2-yl)-L-cysteine ergothioneine-hydroxysulfanolate-lyase

Comments: Contains pyridoxal 5'-phosphate. The enzyme, characterized from the bacterium Mycobacterium smegmatis, cayalyses the last step in the pathway of ergothioneine biosynthesis. The enzyme forms a 2-(hydroxysulfanyl)hercynine intermediate, which is reduced to ergothioneine non-enzymically by a thiol. In vitro, DTT can serve this function.

References:

1. Seebeck, F.P. In vitro reconstitution of Mycobacterial ergothioneine biosynthesis. J. Am. Chem. Soc. 132 (2010) 6632-6633. [PMID: 20420449]

2. Pluskal, T., Ueno, M. and Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS One 9 (2014) e97774. [PMID: 24828577]

3. Song, H., Hu, W., Naowarojna, N., Her, A.S., Wang, S., Desai, R., Qin, L., Chen, X. and Liu, P. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate. Sci Rep 5 (2015) 11870. [PMID: 26149121]

EC 5.4.4.8

Accepted name: linalool isomerase

Reaction: (RS)-linalool = geraniol

For diagram of reaction click here

Other name(s): 3,1-hydroxyl-Δ¹-Δ²-mutase (linalool isomerase)

Systematic name: (RS)-linalool hydroxymutase

Comments: Isolated from the bacterium Thauera linaloolentis grown on (RS)-linalool as the sole source of carbon. Unlike EC 5.4.4.4, geraniol isomerase, which only acts on (S)-linalool, this enzyme acts equally well on both enantiomers.

References:

1. Marmulla, R., Šafarić, B., Markert, S., Schweder, T. and Harder, J. Linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in Thauera linaloolentis 47Lol. BMC Biochem. 17 (2016) 6. [PMID: 26979141]

EC 5.4.99.65

Accepted name: pre-α-onocerin synthase

Reaction: (3S,22S)-2,3:22,23-diepoxy-2,3,22,23-tetrahydrosqualene = pre-α-onocerin

For diagram of reaction click here

Glossary: pre-α-onocerin = (21S)-21,22-epoxypolypoda-8(26)-13,17-trien-3β-ol

Other name(s): LCC

Systematic name: (3S,22S)-2,3:22,23-diepoxy-2,3,22,23-tetrahydrosqualene mutase (cyclizing, pre-α-onocerin-forming)

Comments: Isolated from the plant Lycopodium clavatum. The enzyme does not act on (3S)-2,3-epoxy-2,3-dihydrosqualene and does not form any α-onocerin.

References:

1. Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum. Chembiochem 17 (2016) 288-290. [PMID: 26663356]

EC 5.4.99.66

Accepted name: α-onocerin synthase

Reaction: pre-α-onocerin = α-onocerin

For diagram of reaction click here

Glossary: α-onocerin = 8,14-secogammacera-8(26),14(27)-diene-3β,21α-diol
pre-α-onocerin = (21S)-21,22-epoxypolypoda-8(26)-13,17-trien-3β-ol

Other name(s): LCD

Systematic name: pre-α-onocerin mutase (cyclizing, α-onocerin-forming)

Comments: Isolated from the plant Lycopodium clavatum.

References:

1. Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. Onocerin biosynthesis requires two highly dedicated triterpene cyclases in a fern Lycopodium clavatum. Chembiochem 17 (2016) 288-290. [PMID: 26663356]

EC 5.5.1.28

Accepted name: (–)-kolavenyl diphosphate synthase

Reaction: geranylgeranyl diphosphate = (–)-kolavenyl diphosphate

For diagram of reaction click here

Glossary: (–)-kolavenyl diphosphate = (2E)-5-[(1R,2S,4aS,8aS)-1,2,4a,5-tetramethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl diposphate

Other name(s): SdKPS; TwTPS14; TwTPS10/KPS; SdCPS2; clerodienyl diphosphate synthase; CLPP

Systematic name: (–)-kolavenyl diphosphate lyase (ring-opening)

Comments: Isolated from the hallucinogenic plant Salvia divinorum (seer’s sage) and the medicinal plant Tripterygium wilfordii (thunder god vine).

References:

1. Hansen, N.L., Heskes, A.M., Hamberger, B., Olsen, C.E., Hallstrom, B.M., Andersen-Ranberg, J. and Hamberger, B. The terpene synthase gene family in Tripterygium wilfordii harbors a labdane-type diterpene synthase among the monoterpene synthase TPS-b subfamily. Plant J. 89 (2017) 429-441. [PMID: 27801964]

2. Chen, X., Berim, A., Dayan, F.E. and Gang, D.R. A (–)-kolavenyl diphosphate synthase catalyzes the first step of salvinorin A biosynthesis in Salvia divinorum. J. Exp. Bot. 68 (2017) 1109-1122. [PMID: 28204567]

EC 5.5.1.29

Accepted name: (+)-kolavenyl diphosphate synthase

Reaction: geranylgeranyl diphosphate = (+)-kolavenyl diphosphate

For diagram of reaction click here

Glossary: (+) kolavenyl diphosphate = (2E)-3-methyl-5-[(1R,2S,4aS,8aS)-1,2,4a,5-tetramethyl-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl diphosphate

Systematic name: (+)-kolavenyl-diphosphate lyase (ring-opening)

Comments: Isolated from the bacterium Herpetosiphon aurantiacus.

References:

1. Nakano, C., Oshima, M., Kurashima, N. and Hoshino, T. Identification of a new diterpene biosynthetic gene cluster that produces O-methylkolavelool in Herpetosiphon aurantiacus. Chembiochem 16 (2015) 772-781. [PMID: 25694050]

EC 5.5.1.30

Accepted name: labda-7,13-dienyl diphosphate synthase

Reaction: geranylgeranyl diphosphate = (13E)-labda-7,13-dien-15-yl diphosphate

For diagram of reaction click here

Other name(s): SCLAV_p0490

Systematic name: (13E)-labda-7,13-dien-15-yl-diphosphate lyase (ring-opening)

Comments: Isolated from the bacterium Streptomyces clavuligerus.

References:

1. Yamada, Y., Komatsu, M. and Ikeda, H. Chemical diversity of labdane-type bicyclic diterpene biosynthesis in Actinomycetales microorganisms. J. Antibiot. (Tokyo) 69 (2016) 515-523. [PMID: 26814669]

EC 6.1.3 Cyclo-ligases

EC 6.1.3.1

Accepted name: olefin β-lactone synthetase

Reaction: ATP + a (2R,3S)-2-alkyl-3-hydroxyalkanoate = AMP + diphosphate + a cis-3-alkyl-4-alkyloxetan-2-one

Other name(s): oleC (gene name)

Systematic name: (2R,3S)-2-alkyl-3-hydroxyalkanoate ligase (β-lactone,AMP-forming)

Comments: The enzyme, found in certain bacterial species, participates in a pathway for the production of olefins. It forms a β-lactone. The alkyl group at C² of the substrate ends up as the 3-alkyl group of the product.

References:

1. Sukovich, D.J., Seffernick, J.L., Richman, J.E., Hunt, K.A., Gralnick, J.A. and Wackett, L.P. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Appl. Environ. Microbiol. 76 (2010) 3842-3849. [PMID: 20418444]

2. Frias, J.A., Goblirsch, B.R., Wackett, L.P. and Wilmot, C.M. Cloning, purification, crystallization and preliminary X-ray diffraction of the OleC protein from Stenotrophomonas maltophilia involved in head-to-head hydrocarbon biosynthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1108-1110. [PMID: 20823539]

3. Kancharla, P., Bonnett, S.A. and Reynolds, K.A. Stenotrophomonas maltophilia OleC-catalyzed ATP-dependent formation of long-chain Z-olefins from 2-alkyl-3-hydroxyalkanoic acids. Chembiochem 17 (2016) 1426-1429. [PMID: 27238740]

4. Christenson, J.K., Richman, J.E., Jensen, M.R., Neufeld, J.Y., Wilmot, C.M. and Wackett, L.P. β-Lactone synthetase found in the olefin biosynthesis pathway. Biochemistry 56 (2017) 348-351. [PMID: 28029240]

EC 6.2.1.50

Accepted name: 4-hydroxybenzoate adenylyltransferase FadD22

Reaction: ATP + 4-hydroxybenzoate + holo-[4-hydroxyphenylalkanoate synthase] = AMP + diphosphate + 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase] (overall reaction)
(1a) ATP + 4-hydroxybenzoate = 4-hydroxybenzoyl-adenylate + diphosphate
(1b) 4-hydroxybenzoyl-adenylate + holo-[4-hydroxyphenylalkanoate synthase] = AMP + 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase]

Other name(s): fadD22 (gene name); 4-hydroxybenzoate adenylase

Systematic name: 4-hydroxybenzoate:holo-[4-hydroxyphenylalkanoate synthase] ligase (AMP-forming)

Comments: This mycobacterial enzyme participates in the biosynthesis of phenolphthiocerols. Following the substrate‘s activation by adenylation, it is transferred to an acyl-carrier protein domain within the enzyme, from which it is transferred to EC 2.3.1.261, 4-hydroxyphenylalkanoate synthase.

References:

1. Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715-2725. [PMID: 20553505]

2. Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040-1050. [PMID: 25561717]