An asterisk before'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: (R)-mandelonitrile oxidase
Reaction: (R)-mandelonitrile + O2 = benzoyl cyanide + H2O2
Other name(s): ChuaMOX (gene name)
Systematic name: (R)-mandelonitrile:oxygen oxidoreductase
Comments: Contains FAD. The enzyme, characterized from the millipede Chamberlinius hualienensis, is segregated from its substrate, which is contained in special sacs. The sacs are ruptured during defensive behavior, allowing the enzyme and substrate to mix in special reaction chambers leading to production of the defensive chemical benzoyl cyanide.
References:
1. Ishida, Y., Kuwahara, Y., Dadashipour, M., Ina, A., Yamaguchi, T., Morita, M., Ichiki, Y. and Asano, Y. A sacrificial millipede altruistically protects its swarm using a drone blood enzyme, mandelonitrile oxidase. Sci Rep 6 (2016) 26998. [PMID: 27265180]
*EC 1.3.1.77
Accepted name: anthocyanidin reductase [(2R,3R)-flavan-3-ol-forming]
Reaction: a (2R,3R)-flavan-3-ol + 2 NAD(P)+ = an anthocyanidin with a 3-hydroxy group + 2 NAD(P)H + H+
For diagram of reaction click here.
Other name(s): ANR (gene name) (ambiguous); flavan-3-ol:NAD(P)+ oxidoreductase; anthocyanidin reductase (ambiguous)
Systematic name: (2R,3R)-flavan-3-ol:NAD(P)+ 3,4-oxidoreductase
Comments: The enzyme participates in the flavonoid biosynthesis pathway found in plants. It catalyses the double reduction of anthocyanidins, producing (2R,3R)-flavan-3-ol monomers required for the formation of proanthocyanidins. While the enzyme from the legume Medicago truncatula (MtANR) can use both NADPH and NADH as reductant, that from the crucifer Arabidopsis thaliana (AtANR) uses only NADPH. Also, while the substrate preference of MtANR is cyanidin>pelargonidin>delphinidin, the reverse preference is found with AtANR. cf. EC 1.3.1.112, anthocyanidin reductase [(2S)-flavan-3-ol-forming].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
PDB,
CAS registry number: 93389-48-1
References:
1. Xie, D.Y., Sharma, S.B., Paiva, N.L., Ferreira, D. and Dixon, R.A. Role of anthocyanidin reductase, encoded by BANYULS in plant flavonoid biosynthesis. Science 299 (2003) 396-399. [PMID: 12532018]
2. Xie, D.Y., Sharma, S.B. and Dixon, R.A. Anthocyanidin reductases from Medicago truncatula and Arabidopsis thaliana. Arch. Biochem. Biophys. 422 (2004) 91-102. [PMID: 14725861]
3. Pang, Y., Abeysinghe, I.S., He, J., He, X., Huhman, D., Mewan, K.M., Sumner, L.W., Yun, J. and Dixon, R.A. Functional characterization of proanthocyanidin pathway enzymes from tea and their application for metabolic engineering. Plant Physiol. 161 (2013) 1103-1116. [PMID: 23288883]
EC 1.3.1.112
Accepted name: anthocyanidin reductase [(2S)-flavan-3-ol-forming]
Reaction: (1) a (2S,3R)-flavan-3-ol + 2 NADP+ = an anthocyanidin with a 3-hydroxy group + 2 NADPH + H+
Systematic name: (2S)-flavan-3-ol:NAD(P)+ oxidoreductase
Comments: The enzyme, characterized from Vitis vinifera (grape), participates in the flavonoid biosynthesis pathway. It catalyses the double reduction of anthocyanidins, producing a mixture of (2S,3S)- and (2S,3R)-flavan-3-ols. The enzyme catalyses sequential hydride transfers to C-2 and C-4, respectively. Epimerization at C-3 is achieved by tautomerization that occurs between the two hydride transfers. cf. EC 1.3.1.77, anthocyanidin reductase [(2R,3R)-flavan-3-ol-forming].
References:
1. Gargouri, M., Manigand, C., Mauge, C., Granier, T., Langlois d'Estaintot, B., Cala, O., Pianet, I., Bathany, K., Chaudiere, J. and Gallois, B. Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera. Acta Crystallogr. D Biol. Crystallogr. 65 (2009) 989-1000. [PMID: 19690377]
2. Gargouri, M., Chaudiere, J., Manigand, C., Mauge, C., Bathany, K., Schmitter, J.M. and Gallois, B. The epimerase activity of anthocyanidin reductase from Vitis vinifera and its regiospecific hydride transfers. Biol. Chem. 391 (2010) 219-227. [PMID: 20030585]
EC 1.14.11.54
Accepted name: mRNA N1-methyladenine demethylase
Reaction: N1-methyladenine in mRNA + 2-oxoglutarate + O2 = adenine in mRNA + formaldehyde + succinate + CO2
Other name(s): ALKBH3
Systematic name: mRNA-N1-methyladenine,2-oxoglutarate:oxygen oxidoreductase (formaldehyde-forming)
Comments: Contains iron(II). Catalyses oxidative demethylation of mRNA N1-methyladenine. The enzyme is also involved in alkylation repair in DNA [2].
References:
1. Sundheim, O., Vågbø, C.B., Bjørås, M., Sousa, M.M., Talstad, V., Aas, P.A., Drabløs, F., Krokan, H.E., Tainer, J.A. and Slupphaug, G. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J. 25 (2006) 3389-3397. [PMID: 16858410]
2. Dango, S., Mosammaparast, N., Sowa, M.E., Xiong, L.J., Wu, F., Park, K., Rubin, M., Gygi, S., Harper, J.W. and Shi, Y. DNA unwinding by ASCC3 helicase is coupled to ALKBH3-dependent DNA alkylation repair and cancer cell proliferation. Mol. Cell 44 (2011) 373-384. [PMID: 22055184]
3. Li, X., Xiong, X., Wang, K., Wang, L., Shu, X., Ma, S. and Yi, C. Transcriptome-wide mapping reveals reversible and dynamic N-methyladenosine methylome. Nat. Chem. Biol. (2016) . [PMID: 26863410]
[EC 1.14.13.207 Transferred entry: ipsdienol synthase, now classified as EC 1.14.14.31, ipsdienol synthase (EC 1.14.13.207 created 2015, deleted 2016)]
*EC 1.14.13.217
Accepted name: protodeoxyviolaceinate monooxygenase
Reaction: protodeoxyviolaceinate + NAD(P)H + O2 = protoviolaceinate + NAD(P)+ + H2O
For diagram of reaction click here.
Glossary: protodeoxyviolaceinate = 3,5-di(1H-indol-3-yl)-1H-pyrrole-2-carboxylate
Other name(s): vioD (gene name); protoviolaceinate synthase
Systematic name: protodeoxyviolaceinate,NAD(P)H:O2 oxidoreductase
Comments: The enzyme, characterized from the bacterium Chromobacterium violaceum, participates in the biosynthesis of the violet pigment violacein. The product, protoviolaceinate, can be acted upon by EC 1.14.13.224, violacein synthase, leading to violacein production. However, it is very labile, and in the presence of oxygen can undergo non-enzymic autooxidation to the shunt product proviolacein.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
CAS registry number:
References:
1. Balibar, C.J. and Walsh, C.T. In vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum. Biochemistry 45 (2006) 15444-15457. [PMID: 17176066]
2. Shinoda, K., Hasegawa, T., Sato, H., Shinozaki, M., Kuramoto, H., Takamiya, Y., Sato, T., Nikaidou, N., Watanabe, T. and Hoshino, T. Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function. Chem. Commun. (Camb.) (2007) 4140-4142. [PMID: 17925955]
EC 1.14.13.222
Accepted name: aurachin C monooxygenase/isomerase
Reaction: aurachin C + NAD(P)H + H+ + O2 = 4-hydroxy-2-methyl-3-oxo-4-[(2E,6E)-farnesyl]-3,4-dihydroquinoline 1-oxide + NAD(P)+ + H2O (overall reaction)
For diagram of reaction click here and for mechanism click here.
Glossary: aurachin C = 1-hydroxy-2-methyl-3-[(2E,6E)-farnesyl]-4(1H)-quinolinone
Other name(s): auaG (gene name); aurachin C monooxygenase
Systematic name: aurachin C:NAD(P)H:oxygen oxidoreductase (4-hydroxy-2-methyl-3-oxo-4-farnesyl-3,4-dihydroquinoline-1-oxide-forming)
Comments: The aurachin C monooxygenase from the bacterium Stigmatella aurantiaca accepts both NADH and NADPH as cofactor, but has a preference for NADH. It catalyses the initial steps in the conversion of aurachin C to aurachin B. The FAD-dependent monooxygenase catalyses the epoxidation of the C2-C3 double bond of aurachin C, which is followed by a semipinacol rearrangement, causing migration of the farnesyl group from C3 to C4.
References:
1. Katsuyama, Y., Harmrolfs, K., Pistorius, D., Li, Y. and Muller, R. A semipinacol rearrangement directed by an enzymatic system featuring dual-function FAD-dependent monooxygenase. Angew Chem Int Ed Engl 51 (2012) 9437-9440. [PMID: 22907798]
EC 1.14.13.223
Accepted name: 3-hydroxy-4-methylanthranilyl-[aryl-carrier protein] 5-monooxygenase
Reaction: 3-hydroxy-4-methylanthranilyl-[aryl-carrier protein] + NADH + H+ + O2 = 3,5-dihydroxy-4-methylanthranilyl-[aryl-carrier protein] + NAD+ + H2O
Other name(s): sibG (gene name)
Systematic name: 3-hydroxy-4-methylanthranilyl-[aryl-carrier protein],NADH:oxygen oxidoreductase (5-hydroxylating)
Comments: A flavoprotein (FAD). The enzyme, characterized from the bacterium Streptosporangium sibiricum, is involved in the biosynthesis of the antitumor antibiotic sibiromycin. The enzyme is not active with free 3-hydroxy-4-methylanthranilate.
References:
1. Giessen, T.W., Kraas, F.I. and Marahiel, M.A. A four-enzyme pathway for 3,5-dihydroxy-4-methylanthranilic acid formation and incorporation into the antitumor antibiotic sibiromycin. Biochemistry 50 (2011) 5680-5692. [PMID: 21612226]
EC 1.14.13.224
Accepted name: violacein synthase
Reaction: (1) protoviolaceinate + NAD(P)H + O2 = violaceinate + NAD(P)+ + H2O
For diagram of reaction click here.
Glossary: violacein = 5-(5-hydroxy-3-indolyl)-3-(3-oxinodolylidene)-2-oxopyrroline
Other name(s): proviolaceinate monooxygenase; vioC (gene name)
Systematic name: protoviolaceinate,NAD(P)H:O2 oxidoreductase
Comments: The enzyme, characterized from the bacterium Chromobacterium violaceum, participates in the biosynthesis of the violet pigment violacein. The products, violaceinate and deoxyviolaceinate, undergo non-enzymic autooxidation into violacein and deoxyviolacein, respectively.
References:
1. Balibar, C.J. and Walsh, C.T. In vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum. Biochemistry 45 (2006) 15444-15457. [PMID: 17176066]
2. Shinoda, K., Hasegawa, T., Sato, H., Shinozaki, M., Kuramoto, H., Takamiya, Y., Sato, T., Nikaidou, N., Watanabe, T. and Hoshino, T. Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function. Chem. Commun. (Camb.) (2007) 4140-4142. [PMID: 17925955]
EC 1.14.13.225
Accepted name: F-actin monooxygenase
Reaction: [F-actin]-L-methionine + NADPH + O2 + H+ = [F-actin]-L-methionine-(R)-S-oxide + NADP+ + H2O
Other name(s): MICAL (gene name)
Systematic name: [F-actin]-L-methionine,NADPH:O2 S-oxidoreductase
Comments: The enzyme, characterized from the fruit fly Drosophila melanogaster, is a multi-domain oxidoreductase that acts as an F-actin disassembly factor. The enzyme selectively reduces two L-Met residues of F-actin, causing fragmentation of the filaments and preventing repolymerization [1]. Free methionine is not a substrate [2]. The reaction is stereospecific and generates (R)-sulfoxide [3].
References:
1. Hung, R.J., Yazdani, U., Yoon, J., Wu, H., Yang, T., Gupta, N., Huang, Z., van Berkel, W.J. and Terman, J.R. Mical links semaphorins to F-actin disassembly. Nature 463 (2010) 823-827. [PMID: 20148037]
2. Hung, R.J., Pak, C.W. and Terman, J.R. Direct redox regulation of F-actin assembly and disassembly by Mical. Science 334 (2011) 1710-1713. [PMID: 22116028]
3. Hung, R.J., Spaeth, C.S., Yesilyurt, H.G. and Terman, J.R. SelR reverses Mical-mediated oxidation of actin to regulate F-actin dynamics. Nat. Cell Biol. 15 (2013) 1445-1454. [PMID: 24212093]
EC 1.14.13.226
Accepted name: acetone monooxygenase (methylacetate-forming)
Reaction: acetone + NADPH + H+ + O2 = methylacetate + NADP+ + H2O
Other name(s): acmA (gene name)
Systematic name: acetone,NADPH:oxygen oxidoreductase (methylacetate-forming)
Comments: Contains FAD. The enzyme, characterized from the bacterium Gordonia sp. TY-5, is a Baeyer-Villiger type monooxygenase and participates in a propane utilization pathway.
References:
1. Kotani, T., Yurimoto, H., Kato, N. and Sakai, Y. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J. Bacteriol. 189 (2007) 886-893. [PMID: 17071761]
EC 1.14.13.227
Accepted name: propane 2-monooxygenase
Reaction: propane + NADH + H+ + O2 = propan-2-ol + NAD+ + H2O
Glossary: propan-2-ol = isopropanol
Other name(s): prmABCD (gene names)
Systematic name: propane,NADH:oxygen oxidoreductase (2-hydroxylating)
Comments: The enzyme, characterized from several bacterial strains, is a multicomponent dinuclear iron monooxygenase that includes a hydroxylase, an NADH-dependent reductase, and a coupling protein. The enzyme has several additional activities, including acetone monooxygenase (acetol-forming) and phenol 4-monooxygenase.
References:
1. Kotani, T., Yamamoto, T., Yurimoto, H., Sakai, Y. and Kato, N. Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. J. Bacteriol. 185 (2003) 7120-7128. [PMID: 14645271]
2. Sharp, J.O., Sales, C.M., LeBlanc, J.C., Liu, J., Wood, T.K., Eltis, L.D., Mohn, W.W. and Alvarez-Cohen, L. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 73 (2007) 6930-6938. [PMID: 17873074]
3. Furuya, T., Hirose, S., Osanai, H., Semba, H. and Kino, K. Identification of the monooxygenase gene clusters responsible for the regioselective oxidation of phenol to hydroquinone in mycobacteria. Appl. Environ. Microbiol. 77 (2011) 1214-1220. [PMID: 21183637]
EC 1.14.14.30
Accepted name: isobutylamine N-monooxygenase
Reaction: (1) 2-methylpropanamine + FADH2 + O2 = N-(2-methylpropanoyl)hydroxylamine + FAD + H2O
Glossary: 2-methylpropanamine = isobutylamine
Other name(s): vlmH (gene name)
Systematic name: 2-methylpropanamine,FADH2:O2 N-oxidoreductase
Comments: The enzyme, characterized from the bacterium Streptomyces viridifaciens, is part of a two component system that also includes a flavin reductase, which provides reduced flavin mononucleotide for this enzyme. The enzyme, which is involved in the biosynthesis of the azoxy antibiotic valanimycin, has a similar activity with either FMNH2 or FADH2. It exhibits broad specificity, and also accepts n-propylamine, n-butylamine, sec-butylamine and benzylamine.
References:
1. Parry, R.J. and Li, W. Purification and characterization of isobutylamine N-hydroxylase from the valanimycin producer Streptomyces viridifaciens MG456-hF10. Arch. Biochem. Biophys. 339 (1997) 47-54. [PMID: 9056232]
2. Parry, R.J., Li, W. and Cooper, H.N. Cloning, analysis, and overexpression of the gene encoding isobutylamine N-hydroxylase from the valanimycin producer, Streptomyces viridifaciens. J. Bacteriol. 179 (1997) 409-416. [PMID: 8990292]
3. Parry, R.J. and Li, W. An NADPH:FAD oxidoreductase from the valanimycin producer, Streptomyces viridifaciens. Cloning, analysis, and overexpression. J. Biol. Chem. 272 (1997) 23303-23311. [PMID: 9287340]
EC 1.14.14.31
Accepted name: ipsdienol synthase
Reaction: myrcene + [reduced NADPH—hemoprotein reductase] + O2 = (R)-ipsdienol + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of reaction click here.
Glossary: myrcene = 7-methyl-3-methyleneocta-1,6-diene
Other name(s): myrcene hydroxylase; CYP9T2; CYP9T3
Systematic name: myrcene,NADPH—hemoprotein reductase:O2 oxidoreductase (hydroxylating)
Comments: A cytochrome P-450 heme-thiolate protein. Involved in the insect aggregation pheromone production. Isolated from the pine engraver beetle, Ips pini. A small amount of (S)-ipsdienol is also formed. In vitro it also hydroxylated (+)- and (–)-α-pinene, 3-carene, and (+)-limonene, but not α-phellandrene, (–)-β-pinene, γ-terpinene, or terpinolene.
References:
1. Sandstrom, P., Welch, W.H., Blomquist, G.J. and Tittiger, C. Functional expression of a bark beetle cytochrome P450 that hydroxylates myrcene to ipsdienol. Insect Biochem. Mol. Biol. 36 (2006) 835-845. [PMID: 17046597]
2. Song, M., Kim, A.C., Gorzalski, A.J., MacLean, M., Young, S., Ginzel, M.D., Blomquist, G.J. and Tittiger, C. Functional characterization of myrcene hydroxylases from two geographically distinct Ips pini populations. Insect Biochem. Mol. Biol. 43 (2013) 336-343. [PMID: 23376633]
EC 1.14.14.32
Accepted name: 17α-hydroxyprogesterone deacetylase
Reaction: (1) 17α-hydroxyprogesterone + [reduced NADPH—hemoprotein reductase] + O2 = androstenedione + acetate + [oxidized NADPH—hemoprotein reductase] + H2O
Glossary: androstenedione = androst-4-ene-3,17-dione
Other name(s): C-17/C-20 lyase; 17α-hydroxyprogesterone acetaldehyde-lyase; CYP17; CYP17A1 (gene name); 17α-hydroxyprogesterone 17,20-lyase
Systematic name: 17α-hydroxyprogesterone,NADPH—hemoprotein reductase:oxygen oxidoreductase (17α-hydroxylating, acetate-releasing)
Comments: A microsomal cytochrome P-450 (heme-thiolate) protein that catalyses two independent reactions at the same active site - the 17-hydroxylation of pregnenolone and progesterone, which is part of glucocorticoid hormones biosynthesis (EC 1.14.14.19), and the conversion of the 17-hydroxylated products via a 17,20-lyase reaction to form androstenedione and 3β-hydroxyandrost-5-en-17-one, leading to sex hormone biosynthesis. The activity of this reaction is dependent on the allosteric interaction of the enzyme with cytochrome b5 without any transfer of electrons from the cytochrome [2,4]. The enzymes from different organisms differ in their substrate specificity. While the enzymes from pig, hamster, and rat accept both 17α-hydroxyprogesterone and 17α-hydroxypregnenolone, the enzymes from human, bovine, sheep, goat, and bison do not accept the former, and the enzyme from guinea pig does not accept the latter [1].
References:
1. Gilep, A.A., Estabrook, R.W. and Usanov, S.A. Molecular cloning and heterologous expression in E. coli of cytochrome P45017α. Comparison of structural and functional properties of substrate-specific cytochromes P450 from different species. Biochemistry (Mosc.) 68 (2003) 86-98. [PMID: 12693981]
2. Auchus, R.J., Lee, T.C. and Miller, W.L. Cytochrome b5 augments the 17,20-lyase activity of human P450c17 without direct electron transfer. J. Biol. Chem. 273 (1998) 3158-3165. [PMID: 9452426]
3. Mak, P.J., Gregory, M.C., Denisov, I.G., Sligar, S.G. and Kincaid, J.R. Unveiling the crucial intermediates in androgen production. Proc. Natl. Acad. Sci. USA 112 (2015) 15856-15861. [PMID: 26668369]
4. Simonov, A.N., Holien, J.K., Yeung, J.C., Nguyen, A.D., Corbin, C.J., Zheng, J., Kuznetsov, V.L., Auchus, R.J., Conley, A.J., Bond, A.M., Parker, M.W., Rodgers, R.J. and Martin, L.L. Mechanistic scrutiny identifies a kinetic role for cytochrome b5 regulation of human cytochrome P450c17 (CYP17A1, P450 17A1). PLoS One 10 (2015) e0141252. [PMID: 26587646]
5. Bhatt, M.R., Khatri, Y., Rodgers, R.J. and Martin, L.L. Role of cytochrome b5 in the modulation of the enzymatic activities of cytochrome P450 17α-hydroxylase/17,20-lyase (P450 17A1). J. Steroid Biochem. Mol. Biol. (2016) . [PMID: 26976652]
EC 1.14.21.12
Accepted name: (S)-nandinine synthase
Reaction: (S)-scoulerine + NADPH + H+ + O2 = (S)-nandinine + NADP+ + 2 H2O
For diagram of reaction click here.
Other name(s): CYP719A3
Systematic name: (S)-scoulerine,NADPH:oxygen oxidoreductase [(S)-nandinine-forming]
Comments: A cytochrome P-450 heme-thiolate enzyme catalysing an oxidative reaction that does not incorporate oxygen into the product. Forms the methylenedioxy bridge of the protoberberine alkaloid (S)-nandinine by the oxidative ring closure of adjacent phenolic and methoxy groups of (S)-scoulerine. cf. EC 1.14.21.2, (S)-cheilanthifoline synthase, which catalyses a similar reaction at the other side of the (S)-scoulerine molecule, forming (S)-cheilanthifoline.
References:
1. Ikezawa, N., Iwasa, K. and Sato, F. Molecular cloning and characterization of methylenedioxy bridge-forming enzymes involved in stylopine biosynthesis in Eschscholzia californica. FEBS J. 274 (2007) 1019-1035. [PMID: 17250743]
2. Diaz Chavez, M.L., Rolf, M., Gesell, A. and Kutchan, T.M. Characterization of two methylenedioxy bridge-forming cytochrome P450-dependent enzymes of alkaloid formation in the Mexican prickly poppy Argemone mexicana. Arch. Biochem. Biophys. 507 (2011) 186-193. [PMID: 21094631]
EC 1.17.8 With a flavin as acceptor
EC 1.17.8.1
Accepted name: hydroxysqualene dehydroxylase
Reaction: squalene + FAD + H2O = hydroxysqualene + FADH2
Glossary: hydroxysqualene = (6E,10E,12R,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-12-ol
Other name(s): hpnE (gene name)
Systematic name: squalene:FAD oxidoreductase (hydroxylating)
Comments: This enzyme, isolated from the bacteria Rhodopseudomonas palustris and Zymomonas mobilis, participates, along with EC 2.5.1.103, presqualene diphosphate synthase, and EC 4.2.3.156, hydroxysqualene synthase, in the conversion of all-trans-farnesyl diphosphate to squalene. Eukaryotes achieve the same goal in a single step, catalysed by EC 2.5.1.21, squalene synthase.
References:
1. Pan, J.J., Solbiati, J.O., Ramamoorthy, G., Hillerich, B.S., Seidel, R.D., Cronan, J.E., Almo, S.C. and Poulter, C.D. Biosynthesis of squalene from farnesyl diphosphate in bacteria: three steps catalyzed by three enzymes. ACS Cent Sci 1 (2015) 77-82. [PMID: 26258173]
[EC 1.17.98.1 Deleted entry: bile-acid 7α-dehydroxylase. Now known to be catalyzed by multiple enzymes. (EC 1.17.98.1 created 2005 as EC 1.17.1.6, transferred 2006 to EC 1.17.99.5, transferred 2014 to EC 1.17.98.1, deleted 2016)]
*EC 2.1.1.47
Accepted name: indolepyruvate C-methyltransferase
Reaction: S-adenosyl-L-methionine + (indol-3-yl)pyruvate = S-adenosyl-L-homocysteine + (R)-3-(indol-3-yl)-2-oxobutanoate
Other name(s): ind1 (gene name); indolepyruvate methyltransferase; indolepyruvate 3-methyltransferase; indolepyruvic acid methyltransferase; S-adenosyl-L-methionine:indolepyruvate C-methyltransferase
Systematic name: S-adenosyl-L-methionine:(indol-3-yl)pyruvate C-methyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces griseus, is involved in the biosynthesis of the antibacterial drug indolmycin.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
CAS registry number: 54576-88-4
References:
1. Hornemann, U., Speedie, M.K., Hurley, L.H. and Floss, H.G. Demonstration of a C-methylating enzyme in cell free extracts of indolmycin-producing Streptomyces griseus. Biochem. Biophys. Res. Commun. 39 (1970) 594-599. [PMID: 5490210]
2. Hornemann, U., Hurley, L.H., Speedie, M.K. and Floss, H.G. The biosynthesis of indolmycin. J. Am. Chem. Soc. 93 (1971) 3028-3035. [PMID: 5095271]
3. Speedie, M.K., Hornemann, U. and Floss, H.G. Isolation and characterization of tryptophan transaminase and indolepyruvate C-methyltransferase. Enzymes involved in indolmycin biosynthesis in Streptomyces griseus. J. Biol. Chem. 250 (1975) 7819-7825. [PMID: 809439]
4. Du, Y.L., Alkhalaf, L.M. and Ryan, K.S. In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly. Proc. Natl. Acad. Sci. USA 112 (2015) 2717-2722. [PMID: 25730866]
EC 2.1.1.327
Accepted name: phenazine-1-carboxylate N-methyltransferase
Reaction: S-adenosyl-L-methionine + phenazine-1-carboxylate = S-adenosyl-L-homocysteine + 5-methyl-phenazine-1-carboxylate
Other name(s): phzM (gene name)
Systematic name: S-adenosyl-L-methionine:phenazine-1-carboxylate 5-N-methyltransferase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is involved in the biosynthesis of pyocyanin, a toxin produced and secreted by the organism. The enzyme is active in vitro only in the presence of EC 1.14.13.218, 5-methylphenazine-1-carboxylate 1-monooxygenase.
References:
1. Parsons, J.F., Greenhagen, B.T., Shi, K., Calabrese, K., Robinson, H. and Ladner, J.E. Structural and functional analysis of the pyocyanin biosynthetic protein PhzM from Pseudomonas aeruginosa. Biochemistry 46 (2007) 1821-1828. [PMID: 17253782]
EC 2.1.1.328
Accepted name: N-demethylindolmycin N-methyltransferase
Reaction: S-adenosyl-L-methionine + N-demethylindolmycin = S-adenosyl-L-homocysteine + indolmycin
Glossary: indolmycin = (5S)-5-[(1R)-1-(indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazolin-4(5H)-one
Other name(s): ind7 (gene name)
Systematic name: S-adenosyl-L-methionine:N-demethylindolmycin N-methyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces griseus, catalyses the ultimate reaction in the biosynthesis of indolmycin, an antibacterial drug that inhibits the bacterial tryptophan—tRNA ligase (EC 6.1.1.2).
References:
1. Du, Y.L., Alkhalaf, L.M. and Ryan, K.S. In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly. Proc. Natl. Acad. Sci. USA 112 (2015) 2717-2722. [PMID: 25730866]
*EC 2.4.1.135
Accepted name: galactosylgalactosylxylosylprotein 3-β-glucuronosyltransferase
Reaction: UDP-α-D-glucuronate + [protein]-3-O-(β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl)-L-serine = UDP + [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine
For diagram of reaction click here.
Glossary: [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine = [protein]-3-O-(β-D-glucuronosyl-(1→3)-β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl)-L-serine
Other name(s): glucuronosyltransferase I; uridine diphosphate glucuronic acid:acceptor glucuronosyltransferase; UDP-glucuronate:3-β-D-galactosyl-4-β-D-galactosyl-O-β-D-xylosyl-protein D-glucuronosyltransferase; UDP-glucuronate:3-β-D-galactosyl-4-β-D-galactosyl-O-β-D-xylosylprotein D-glucuronosyltransferase
Systematic name: UDP-α-D-glucuronate:[protein]-3-O-(β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl)-L-serine D-glucuronosyltransferase (configuration-inverting)
Comments: Involved in the biosynthesis of the linkage region of glycosaminoglycan chains as part of proteoglycan biosynthesis (chondroitin, dermatan and heparan sulfates). Requires Mn2+.
Links to other databases:
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EXPASY,
KEGG,
MetaCyc,
PDB,
CAS registry number: 227184-75-0
References:
1. Helting, J. and Roden, L. Biosynthesis of chondroitin sulfate. II. Glucuronosyl transfer in the formation of the carbohydrate-protein linkage region. J. Biol. Chem. 244 (1969) 2799-2805. [PMID: 5770003]
2. Helting, T. Biosynthesis of heparin. Solubilization and partial purification of uridine diphosphate glucuronic acid: acceptor glucuronosyltransferase from mouse mastocytoma. J. Biol. Chem. 247 (1972) 4327-4332. [PMID: 4260846]
3. Kitagawa, H., Tone, Y., Tamura, J., Neumann, K.W., Ogawa, T., Oka, S., Kawasaki, T. and Sugahara, K. Molecular cloning and expression of glucuronyltransferase I involved in the biosynthesis of the glycosaminoglycan-protein linkage region of proteoglycans. J. Biol. Chem. 273 (1998) 6615-6618. [PMID: 9506957]
*EC 2.4.1.187
Accepted name: N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-β-D-mannosaminyltransferase
Reaction: UDP-N-acetyl-α-D-mannosamine + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + N-acetyl-β-D-mannosaminyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): uridine diphosphoacetyl-mannosamineacetylglucosaminylpyrophosphorylundecaprenol acetylmannosaminyltransferase; N-acetylmannosaminyltransferase; UDP-N-acetylmannosamine:N-acetylglucosaminyl diphosphorylundecaprenol N-acetylmannosaminyltransferase; UDP-N-acetyl-D-mannosamine:N-acetyl-β-D-glucosaminyldiphosphoundecaprenol β-1,4-N-acetylmannosaminyltransferase; UDP-N-acetyl-D-mannosamine:N-acetyl-β-D-glucosaminyldiphosphoundecaprenol 4-β-N-acetylmannosaminyltransferase; tagA (gene name); tarA (gene name); UDP-N-acetyl-α-D-mannosamine:N-acetyl-β-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 4-β-N-acetylmannosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-mannosamine:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 4-β-N-acetylmannosaminyltransferase (configuration-inverting)
Comments: Involved in the biosynthesis of teichoic acid linkage units in bacterial cell walls.
Links to other databases:
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EXPASY,
KEGG,
MetaCyc,
CAS registry number: 118731-82-1
References:
1. Murazumi, N., Kumita, K., Araki, Y. and Ito, E. Partial purification and properties of UDP-N-acetylmannosamine:N-acetylglucosaminyl pyrophosphorylundecaprenol N-acetylmannosaminyltransferase from Bacillus subtilis. J. Biochem. (Tokyo) 104 (1988) 980-984. [PMID: 2977387]
2. Ginsberg, C., Zhang, Y.H., Yuan, Y. and Walker, S. In vitro reconstitution of two essential steps in wall teichoic acid biosynthesis. ACS Chem. Biol. 1 (2006) 25-28. [PMID: 17163636]
3. Zhang, Y.H., Ginsberg, C., Yuan, Y. and Walker, S. Acceptor substrate selectivity and kinetic mechanism of Bacillus subtilis TagA. Biochemistry 45 (2006) 10895-10904. [PMID: 16953575]
EC 2.5.1.133
Accepted name: bacteriochlorophyll a synthase
Reaction: geranylgeranyl diphosphate + bacteriochlorophyllide a = geranylgeranyl-bacteriochlorophyllide a + diphosphate
For diagram of reaction click here.
Other name(s): bchG (gene name)
Systematic name: geranylgeranyl-diphosphate:bacteriochlorophyllide-a geranylgeranytransferase
Comments: The enzyme catalyses the addition of a geranylgeranyl hydrophobic chain to bacteriochlorophyllide a via an ester bond with the 17-propionate residue. The side chain is later modified to a phytyl chain, resulting in bacteriochlorophyll a.
References:
1. Oster, U., Bauer, C.E. and Rüdiger, W. Characterization of chlorophyll a and bacteriochlorophyll a synthases by heterologous expression in Escherichia coli. J. Biol. Chem. 272 (1997) 9671-9676. [PMID: 9092496]
2. Addlesee, H.A., Fiedor, L. and Hunter, C.N. Physical mapping of bchG, orf427, and orf177 in the photosynthesis gene cluster of Rhodobacter sphaeroides: functional assignment of the bacteriochlorophyll synthetase gene. J. Bacteriol. 182 (2000) 3175-3182. [PMID: 10809697]
3. Garcia-Gil, L.J., Gich, F.B. and Fuentes-Garcia, X. A comparative study of bchG from green photosynthetic bacteria. Arch. Microbiol. 179 (2003) 108-115. [PMID: 12560989]
4. Saga, Y., Hirota, K., Harada, J. and Tamiaki, H. In vitro enzymatic activities of bacteriochlorophyll a synthase derived from the green sulfur photosynthetic bacterium Chlorobaculum tepidum. Biochemistry 54 (2015) 4998-5005. [PMID: 26258685]
EC 2.5.1.134
Accepted name: cystathionine β-synthase (O-acetyl-L-serine)
Reaction: O-acetyl-L-serine + L-homocysteine = L-cystathionine + acetate
For diagram of reaction click here.
Other name(s): MccB; O-acetylserine dependent cystathionine β-synthase
Systematic name: O-acetyl-L-serine:L-homocysteine 2-amino-2-carboxyethyltransferase
Comments: A pyridoxal 5'-phosphate protein. The enzyme, purified from the bacterium Bacillus subtilis, also has a low activity with L-serine (cf. EC 4.2.1.22, cystathionine β-synthase).
References:
1. Hullo, M.F., Auger, S., Soutourina, O., Barzu, O., Yvon, M., Danchin, A. and Martin-Verstraete, I. Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J. Bacteriol. 189 (2007) 187-197. [PMID: 17056751]
*EC 2.7.1.27
Accepted name: erythritol kinase (D-erythritol 4-phosphate-forming)
Reaction: ATP + erythritol = ADP + D-erythritol 4-phosphate
Other name(s): erythritol kinase (phosphorylating) (ambiguous)
Systematic name: ATP:erythritol 4-phosphotransferase
Comments: The enzyme has been characterized from the bacterium Propionibacterium acidipropionici (previously known as Propionibacterium pentosaceum). cf. EC 2.7.1.215, erythritol kinase (L-erythritol 4-phosphate-forming).
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CAS registry number: 9030-64-2
References:
1. Shetter, J.K. Formation of D-erythritol 4-phosphate by Propionibacterium pentosaceum. J. Am. Chem. Soc. 78 (1956) 3722-3723.
2. Holten, D. and Fromm, H.J. Purification and properties of erythritol kinase from Propionibacterium pentosaceum. J. Biol. Chem. 236 (1961) 2581-2584. [PMID: 13908588]
*EC 2.7.1.91
Accepted name: sphingosine kinase
Reaction: ATP + a sphingoid base = ADP + a sphingoid base 1-phosphate
Other name(s): SPHK1 (gene name); SPHK2 (gene name); dihydrosphingosine kinase; dihydrosphingosine kinase (phosphorylating); sphingosine kinase (phosphorylating); sphingoid base kinase; sphinganine kinase; ATP:sphinganine 1-phosphotransferase
Systematic name: ATP:sphingoid base 1-phosphotransferase
Comments: The enzyme is involved in the production of sphingolipid metabolites. It phosphorylates various sphingoid long-chain bases, such as sphingosine, D-erythro-dihydrosphingosine (sphinganine), phytosphingosine (4-hydroxysphinganine), 4-hydroxy-8-sphingenine, 4,8-sphingadienine and D-threo-dihydrosphingosine and L-threo-dihydrosphingosine. The exact substrate range depends on the species.
Links to other databases:
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EXPASY,
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CAS registry number: 50864-48-7
References:
1. Stoffel, W., Heimann, G. and Hellenbroich, B. Sphingosine kinase in blood platelets. Hoppe-Seyler's Z. Physiol. Chem. 354 (1973) 562-566. [PMID: 4372149]
2. Stoffel, W., Bauer, E. and Stahl, J. The metabolism of sphingosine bases in Tetrahymena pyriformis. Sphingosine kinase and sphingosine-1-phosphate lyase. Hoppe-Seyler's Z. Physiol. Chem. 355 (1974) 61-74. [PMID: 4373374]
3. Nagiec, M.M., Skrzypek, M., Nagiec, E.E., Lester, R.L. and Dickson, R.C. The LCB4 (YOR171c) and LCB5 (YLR260w) genes of Saccharomyces encode sphingoid long chain base kinases. J. Biol. Chem. 273 (1998) 19437-19442. [PMID: 9677363]
4. Kohama, T., Olivera, A., Edsall, L., Nagiec, M.M., Dickson, R. and Spiegel, S. Molecular cloning and functional characterization of murine sphingosine kinase. J. Biol. Chem. 273 (1998) 23722-23728. [PMID: 9726979]
5. Liu, H., Sugiura, M., Nava, V.E., Edsall, L.C., Kono, K., Poulton, S., Milstien, S., Kohama, T. and Spiegel, S. Molecular cloning and functional characterization of a novel mammalian sphingosine kinase type 2 isoform. J. Biol. Chem. 275 (2000) 19513-19520. [PMID: 10751414]
6. Worrall, D., Liang, Y.K., Alvarez, S., Holroyd, G.H., Spiegel, S., Panagopulos, M., Gray, J.E. and Hetherington, A.M. Involvement of sphingosine kinase in plant cell signalling. Plant J. 56 (2008) 64-72. [PMID: 18557834]
EC 2.7.1.211
Accepted name: protein-Nπ-phosphohistidine—sucrose phosphotransferase
Reaction: [protein]-Nπ-phospho-L-histidine + sucrose[side 1] = [protein]-L-histidine + sucrose 6G-phosphate[side 2]
Other name(s): scrAB (gene names); sucrose PTS permease; EIIScr; Enzyme IIScr
Systematic name: protein-Nπ-phospho-L-histidine:sucrose Nπ-phosphotransferase
Comments: This enzyme is a component (known as enzyme II) of a phosphoenolpyruvate (PEP)-dependent, sugar transporting phosphotransferase system (PTS). The system, which is found only in prokaryotes, simultaneously transports its substrate from the periplasm or extracellular space into the cytoplasm and phosphorylates it. The phosphate donor, which is shared among the different systems, is a phospho-carrier protein of low molecular mass that has been phosphorylated by EC 2.7.3.9 (phosphoenolpyruvate—protein phosphotransferase). Enzyme II, on the other hand, is specific for a particular substrate, although in some cases alternative substrates can be transported with lower efficiency. The reaction involves a successive transfer of the phosphate group to several amino acids within the enzyme before the final transfer to the substrate.
References:
1. St Martin, E.J. and Wittenberger, C.L. Characterization of a phosphoenolpyruvate-dependent sucrose phosphotransferase system in Streptococcus mutans. Infect. Immun. 24 (1979) 865-868. [PMID: 468378]
2. Lunsford, R.D. and Macrina, F.L. Molecular cloning and characterization of scrB, the structural gene for the Streptococcus mutans phosphoenolpyruvate-dependent sucrose phosphotransferase system sucrose-6-phosphate hydrolase. J. Bacteriol. 166 (1986) 426-434. [PMID: 3009399]
3. Fouet, A., Arnaud, M., Klier, A. and Rapoport, G. Bacillus subtilis sucrose-specific enzyme II of the phosphotransferase system: expression in Escherichia coli and homology to enzymes II from enteric bacteria. Proc. Natl. Acad. Sci. USA 84 (1987) 8773-8777. [PMID: 3122206]
4. Sato, Y., Poy, F., Jacobson, G.R. and Kuramitsu, H.K. Characterization and sequence analysis of the scrA gene encoding enzyme IIScr of the Streptococcus mutans phosphoenolpyruvate-dependent sucrose phosphotransferase system. J. Bacteriol. 171 (1989) 263-271. [PMID: 2536656]
5. Titgemeyer, F., Jahreis, K., Ebner, R. and Lengeler, J.W. Molecular analysis of the scrA and scrB genes from Klebsiella pneumoniae and plasmid pUR400, which encode the sucrose transport protein Enzyme II Scr of the phosphotransferase system and a sucrose-6-phosphate invertase. Mol. Gen. Genet. 250 (1996) 197-206. [PMID: 8628219]
6. Jiang, L., Cai, J., Wang, J., Liang, S., Xu, Z. and Yang, S.T. Phosphoenolpyruvate-dependent phosphorylation of sucrose by Clostridium tyrobutyricum ZJU 8235: evidence for the phosphotransferase transport system. Bioresour. Technol. 101 (2010) 304-309. [PMID: 19726178]
EC 2.7.1.212
Accepted name: α-D-ribose-1-phosphate 5-kinase (ADP)
Reaction: ADP + α-D-ribose-1-phosphate = AMP + α-D-ribose 1,5-bisphosphate
Systematic name: ADP:α-D-ribose-1-phosphate 5-phosphotransferase
Comments: The enzyme, characterized from the archaeon Thermococcus kodakarensis, participates in an archaeal pathway for nucleoside degradation.
References:
1. Aono, R., Sato, T., Imanaka, T. and Atomi, H. A pentose bisphosphate pathway for nucleoside degradation in Archaea. Nat. Chem. Biol. 11 (2015) 355-360. [PMID: 25822915]
EC 2.7.1.213
Accepted name: cytidine kinase
Reaction: ATP + cytidine = ADP + CMP
Systematic name: ATP:cytidine 5'-phosphotransferase
Comments: The enzyme, characterized from the archaeon Thermococcus kodakarensis, participates in a pathway for nucleoside degradation. The enzyme can also act on deoxycytidine and uridine, but unlike EC 2.7.1.48, uridine kinase, it is most active with cytidine.
References:
1. Aono, R., Sato, T., Imanaka, T. and Atomi, H. A pentose bisphosphate pathway for nucleoside degradation in Archaea. Nat. Chem. Biol. 11 (2015) 355-360. [PMID: 25822915]
EC 2.7.1.214
Accepted name: C7-cyclitol 7-kinase
Reaction: (1) ATP + valienone = ADP + valienone 7-phosphate
Glossary: valienone = (4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one
Other name(s): valC (gene name); vldC (gene name)
Systematic name: ATP:C7-cyclitol 7-phosphotransferase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus var. jinggangensis, is involved in the biosynthesis of the antifungal agent validamycin A.
References:
1. Minagawa, K., Zhang, Y., Ito, T., Bai, L., Deng, Z. and Mahmud, T. ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the antifungal agent validamycin A. Chembiochem 8 (2007) 632-641. [PMID: 17335096]
EC 2.7.1.215
Accepted name: erythritol kinase (D-erythritol 1-phosphate-forming)
Reaction: ATP + erythritol = ADP + D-erythritol 1-phosphate
Other name(s): eryA (gene name)
Systematic name: ATP:erythritol 1-phosphotransferase
Comments: The enzyme, characterized from the pathogenic bacterium Brucella abortus, which causes brucellosis in livestock, participates in erythritol catabolism. cf. EC 2.7.1.27, erythritol kinase (D-erythritol 4-phosphate-forming).
References:
1. Sperry, J.F. and Robertson, D.C. Erythritol catabolism by Brucella abortus. J. Bacteriol. 121 (1975) 619-630. [PMID: 163226]
2. Lillo, A.M., Tetzlaff, C.N., Sangari, F.J. and Cane, D.E. Functional expression and characterization of EryA, the erythritol kinase of Brucella abortus, and enzymatic synthesis of L-erythritol-4-phosphate. Bioorg. Med. Chem. Lett. 13 (2003) 737-739. [PMID: 12639570]
*EC 2.7.4.7
Accepted name: phosphooxymethylpyrimidine kinase
Reaction: ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
For diagram of reaction click here.
Other name(s): hydroxymethylpyrimidine phosphokinase; ATP:4-amino-2-methyl-5-phosphooxymethylpyrimidine phosphotransferase; ATP:(4-amino-2-methylpyrimidin-5-yl)methyl-phosphate phosphotransferase; phosphomethylpyrimidine kinase
Systematic name: ATP:4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine phosphotransferase
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CAS registry number: 37278-18-5
References:
1. Lewin, L.M. and Brown, G.M. The biosynthesis of thiamine. III. Mechanism of enzymatic formation of the pyrophosphate ester of 2-methyl-4-amino-5-hydroxymethylpyrimidine. J. Biol. Chem. 236 (1961) 2768-2771.
*EC 2.7.7.42
Accepted name: [glutamine synthetase] adenylyltransferase
Reaction: ATP + [glutamine synthetase]-L-tyrosine = diphosphate + [glutamine synthetase]-O4-(5'-adenylyl)-L-tyrosine
Other name(s): glutamine-synthetase adenylyltransferase; ATP:glutamine synthetase adenylyltransferase; adenosine triphosphate:glutamine synthetase adenylyltransferase; ATP:[L-glutamate:ammonia ligase (ADP-forming)] adenylyltransferase; ATP:[L-glutamate:ammonia ligase (ADP-forming)]-L-tyrosine adenylyltransferase; [glutamate—ammonia-ligase] adenylyltransferase
Systematic name: ATP:[glutamine synthetase]-L-tyrosine adenylyltransferase
Comments: This bacterial enzyme adenylates a tyrosine residue of EC 6.3.1.2, glutamine synthetase. The enzyme is bifunctional, and also catalyses a reaction that removes the adenyl group from the modified tyrosine residue (cf. EC 2.7.7.89, [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase) [7,8]. The two activities are present on separate domains.
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EXPASY,
GTD,
KEGG,
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PDB,
CAS registry number: 9077-66-1
References:
1. Ebner, E., Wolf, D., Gancedo, C., Elsasser, S. and Holzer, H. ATP: glutamine synthetase adenylyltransferase from Escherichia coli B. Purification and properties. Eur. J. Biochem. 14 (1970) 535-544. [PMID: 4920894]
2. Kingdon, H.S., Shapiro, B.M. and Stadtman, E.R. Regulation of glutamine synthetase. 8. ATP: glutamine synthetase adenylyltransferase, an enzyme that catalyzes alterations in the regulatory properties of glutamine synthetase. Proc. Natl. Acad. Sci. USA 58 (1967) 1703-1710. [PMID: 4867671]
3. Mecke, D., Wulff, K. and Holzer, H. Characterization of a glutamine synthetase inactivating enzyme from Escherichia coli. Biochem. Biophys. Res. Commun. 24 (1966) 452-458. [PMID: 5338440]
4. Mecke, D., Wulff, K. and Holzer, H. Metabolit-induzierte Inaktivierung von Glutaminsynthetase aus Escherichia coli im zellfreien System. Biochim. Biophys. Acta 128 (1966) 559-567.
5. Shapiro, B.M. and Stadtman, E.R. 5'-Adenylyl-O-tyrosine. The novel phosphodiester residue of adenylylated glutamine synthetase from Escherichia coli. J. Biol. Chem. 243 (1968) 3769-3771. [PMID: 4298074]
6. Wolf, D., Ebner, E. and Hinze, H. Inactivation, stabilization and some properties of ATP: glutamine synthetase adenylyltransferase from Escherichia coli B. Eur. J. Biochem. 25 (1972) 239-244. [PMID: 4402680]
7. Jaggi, R., van Heeswijk, W.C., Westerhoff, H.V., Ollis, D.L. and Vasudevan, S.G. The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction. EMBO J. 16 (1997) 5562-5571. [PMID: 9312015]
8. Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Huber, T., Vasudevan, S.G. and Ollis, D.L. Structure of the N-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase. Structure 12 (2004) 861-869. [PMID: 15130478]
*EC 2.7.7.89
Accepted name: [glutamine synthetase]-adenylyl-L-tyrosine phosphorylase
Reaction: [glutamine synthetase]-O4-(5'-adenylyl)-L-tyrosine + phosphate = [glutamine synthetase]-L-tyrosine + ADP
Other name(s): adenylyl-[glutamine—synthetase]-deadenylase; [L-glutamate:ammonia ligase (ADP-forming)]-O4-(5'-adenylyl)-L-tyrosine:phosphate adenylyltransferase; [glutamate—ammonia ligase]-adenylyl-L-tyrosine phosphorylase
Systematic name: [glutamine synthetase]-O4-(5'-adenylyl)-L-tyrosine:phosphate adenylyltransferase
Comments: This bacterial enzyme removes an adenylyl group from a modified tyrosine residue of EC 6.3.1.2, glutamine synthetase. The enzyme is bifunctional, and also performs the adenylation of this residue (cf. EC 2.7.7.42, [glutamine synthetase] adenylyltransferase) [3,5]. The two activities are present on separate domains.
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BRENDA,
EXPASY,
KEGG,
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CAS registry number:
References:
1. Anderson, W.B. and Stadtman, E.R. Glutamine synthetase deadenylation: a phosphorolytic reaction yielding ADP as nucleotide product. Biochem. Biophys. Res. Commun. 41 (1970) 704-709. [PMID: 4920873]
2. Anderson, W.B. and Stadtman, E.R. Purification and functional roles of the P I and P II components of Escherichia coli glutamine synthetase deadenylylation system. Arch. Biochem. Biophys. 143 (1971) 428-443. [PMID: 4934180]
3. Jaggi, R., van Heeswijk, W.C., Westerhoff, H.V., Ollis, D.L. and Vasudevan, S.G. The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction. EMBO J. 16 (1997) 5562-5571. [PMID: 9312015]
4. Xu, Y., Wen, D., Clancy, P., Carr, P.D., Ollis, D.L. and Vasudevan, S.G. Expression, purification, crystallization, and preliminary X-ray analysis of the N-terminal domain of Escherichia coli adenylyl transferase. Protein Expr. Purif. 34 (2004) 142-146. [PMID: 14766310]
5. Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Huber, T., Vasudevan, S.G. and Ollis, D.L. Structure of the N-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase. Structure 12 (2004) 861-869. [PMID: 15130478]
EC 2.7.7.91
Accepted name: valienol-1-phosphate guanylyltransferase
Reaction: GTP + valienol 1-phosphate = diphosphate + GDP-valienol
Glossary: valienol 1-phosphate = (1S,4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl phosphate
Other name(s): vldB (gene name)
Systematic name: GTP:valienol 1-phosphate guanylyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus subsp. limoneus, is involved in the biosynthesis of the antifungal agent validamycin A.
References:
1. Yang, J., Xu, H., Zhang, Y., Bai, L., Deng, Z. and Mahmud, T. Nucleotidylation of unsaturated carbasugar in validamycin biosynthesis. Org. Biomol. Chem. 9 (2011) 438-449. [PMID: 20981366]
2. Asamizu, S., Yang, J., Almabruk, K.H. and Mahmud, T. Pseudoglycosyltransferase catalyzes nonglycosidic C-N coupling in validamycin a biosynthesis. J. Am. Chem. Soc. 133 (2011) 12124-12135. [PMID: 21766819]
EC 2.7.7.92
Accepted name: 3-deoxy-D-glycero-D-galacto-nononate cytidylyltransferase
Reaction: CTP + 3-deoxy-D-glycero-D-galacto-nononate = diphosphate + CMP-3-deoxy-D-glycero-D-galacto-nononate
Systematic name: CTP:3-deoxy-D-glycero-D-galacto-nononate cytidylyltransferase
Comments: The enzyme is part of the biosynthesis pathway of the sialic acid 3-deoxy-D-glycero-D-galacto-nononate (KDN). KDN is abundant in extracellular glycoconjugates of lower vertebrates such as fish and amphibians, but is also found in the capsular polysaccharides of bacteria that belong to the Bacteroides genus.
References:
1. Terada, T., Kitazume, S., Kitajima, K., Inoue, S., Ito, F., Troy, F.A. and Inoue, Y. Synthesis of CMP-deaminoneuraminic acid (CMP-KDN) using the CTP:CMP-3-deoxynonulosonate cytidylyltransferase from rainbow trout testis. Identification and characterization of a CMP-KDN synthetase. J. Biol. Chem. 268 (1993) 2640-2648. [PMID: 8381411]
2. Terada, T., Kitajima, K., Inoue, S., Koppert, K., Brossmer, R. and Inoue, Y. Substrate specificity of rainbow trout testis CMP-3-deoxy-D-glycero-D-galacto-nonulosonic acid (CMP-Kdn) synthetase: kinetic studies of the reaction of natural and synthetic analogues of nonulosonic acid catalyzed by CMP-Kdn synthetase. Eur. J. Biochem. 236 (1996) 852-855. [PMID: 8665905]
3. Nakata, D., Munster, A.K., Gerardy-Schahn, R., Aoki, N., Matsuda, T. and Kitajima, K. Molecular cloning of a unique CMP-sialic acid synthetase that effectively utilizes both deaminoneuraminic acid (KDN) and N-acetylneuraminic acid (Neu5Ac) as substrates. Glycobiology 11 (2001) 685-692. [PMID: 11479279]
4. Tiralongo, J., Fujita, A., Sato, C., Kitajima, K., Lehmann, F., Oschlies, M., Gerardy-Schahn, R. and Munster-Kuhnel, A.K. The rainbow trout CMP-sialic acid synthetase utilises a nuclear localization signal different from that identified in the mouse enzyme. Glycobiology 17 (2007) 945-954. [PMID: 17580313]
5. Wang, L., Lu, Z., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN). Chem. Biol. 15 (2008) 893-897. [PMID: 18804026]
EC 2.7.7.93
Accepted name: phosphonoformate cytidylyltransferase
Reaction: CTP + phosphonoformate = CMP-5'-phosphonoformate + diphosphate
Other name(s): phpF (gene name)
Systematic name: CTP:phosphonoformate cytidylyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, participates in the biosynthesis of the herbicide antibiotic bialaphos. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase.
References:
1. Blodgett, J.A., Thomas, P.M., Li, G., Velasquez, J.E., van der Donk, W.A., Kelleher, N.L. and Metcalf, W.W. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat. Chem. Biol. 3 (2007) 480-485. [PMID: 17632514]
EC 2.7.7.94
Accepted name: 4-hydroxyphenylalkanoate adenylyltransferase
Reaction: (1) ATP + 17-(4-hydroxyphenyl)heptadecanoate = diphosphate + 17-(4-hydroxyphenyl)heptadecanoyl adenylate
Other name(s): fadD29 (gene name); 4-hydroxyphenylalkanoate adenylase
Systematic name: ATP:4-hydroxyphenylalkanoate adenylyltransferase
Comments: The 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 the phenolphthiocerol/phthiocerol polyketide 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]
*EC 2.7.8.5
Accepted name: CDP-diacylglycerol—glycerol-3-phosphate 1-phosphatidyltransferase
Reaction: CDP-diacylglycerol + sn-glycerol 3-phosphate = CMP + 1-(3-sn-phosphatidyl)-sn-glycerol 3-phosphate
Other name(s): glycerophosphate phosphatidyltransferase; 3-phosphatidyl-1'-glycerol-3'-phosphate synthase; CDPdiacylglycerol:glycerol-3-phosphate phosphatidyltransferase; cytidine 5'-diphospho-1,2-diacyl-sn-glycerol (CDP-diglyceride):sn-glycerol-3-phosphate phosphatidyltransferase; phosphatidylglycerophosphate synthase; phosphatidylglycerolphosphate synthase; PGP synthase; CDP-diacylglycerol-sn-glycerol-3-phosphate 3-phosphatidyltransferase; CDP-diacylglycerol:sn-glycero-3-phosphate phosphatidyltransferase; glycerol phosphate phosphatidyltransferase; glycerol 3-phosphate phosphatidyltransferase; phosphatidylglycerol phosphate synthase; phosphatidylglycerol phosphate synthetase; phosphatidylglycerophosphate synthetase; sn-glycerol-3-phosphate phosphatidyltransferase
Systematic name: CDP-diacylglycerol:sn-glycerol-3-phosphate 1-(3-sn-phosphatidyl)transferase
Comments: The enzyme catalyses the committed step in the biosynthesis of acidic phospholipids known by the common names phophatidylglycerols and cardiolipins.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
CAS registry number: 9068-49-9
References:
1. Hirabayashi, T. Larson, T.J. and Dowhan, W. Membrane-associated phosphatidylglycerophosphate synthetase from Escherichia coli: Purification by substrate affinity chromatography on cytidine 5'-diphospho-1,2-diacyl-sn-glycerol sepharose. Biochemistry 15 (1976) 5205-5211. [PMID: 793612]
2. Bleasdale, J.E. and Johnston, J.M. CMP-dependent incorporation of [14C]glycerol 3-phosphate into phosphatidylglycerol and phosphatidylglycerol phosphate by rabbit lung microsomes. Biochim. Biophys. Acta 710 (1982) 377-390. [PMID: 7074121]
3. Dowhan, W. Phosphatidylglycerophosphate synthase from Escherichia coli. Methods Enzymol. 209 (1992) 313-321. [PMID: 1323047]
4. Kawasaki, K., Kuge, O., Chang, S.C., Heacock, P.N., Rho, M., Suzuki, K., Nishijima, M. and Dowhan, W. Isolation of a chinese hamster ovary (CHO) cDNA encoding phosphatidylglycerophosphate (PGP) synthase, expression of which corrects the mitochondrial abnormalities of a PGP synthase-defective mutant of CHO-K1 cells. J. Biol. Chem. 274 (1999) 1828-1834. [PMID: 9880566]
5. Muller, F. and Frentzen, M. Phosphatidylglycerophosphate synthases from Arabidopsis thaliana. FEBS Lett. 509 (2001) 298-302. [PMID: 11741606]
6. Babiychuk, E., Muller, F., Eubel, H., Braun, H.P., Frentzen, M. and Kushnir, S. Arabidopsis phosphatidylglycerophosphate synthase 1 is essential for chloroplast differentiation, but is dispensable for mitochondrial function. Plant J. 33 (2003) 899-909. [PMID: 12609031]
*EC 2.8.1.10
Accepted name: thiazole synthase
Reaction: 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-[sulfur-carrier protein ThiS] = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS] + 2 H2O
For diagram of reaction click here.
Glossary: cThz*-P = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
Other name(s): thiG (gene name)
Systematic name: 1-deoxy-D-xylulose 5-phosphate:thiol sulfurtransferase
Comments: H2S can provide the sulfur in vitro. Part of the pathway for thiamine biosynthesis.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
CAS registry number:
References:
1. Park, J.H., Dorrestein, P.C., Zhai, H., Kinsland, C., McLafferty, F.W. and Begley, T.P. Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry 42 (2003) 12430-12438. [PMID: 14567704]
2. Dorrestein, P.C., Zhai, H., McLafferty, F.W. and Begley, T.P. The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. Chem. Biol. 11 (2004) 1373-1381. [PMID: 15489164]
3. Dorrestein, P.C., Zhai, H., Taylor, S.V., McLafferty, F.W. and Begley, T.P. The biosynthesis of the thiazole phosphate moiety of thiamin (vitamin B1): the early steps catalyzed by thiazole synthase. J. Am. Chem. Soc. 126 (2004) 3091-3096. [PMID: 15012138]
4. Settembre, E.C., Dorrestein, P.C., Zhai, H., Chatterjee, A., McLafferty, F.W., Begley, T.P. and Ealick, S.E. Thiamin biosynthesis in Bacillus subtilis: structure of the thiazole synthase/sulfur carrier protein complex. Biochemistry 43 (2004) 11647-11657. [PMID: 15362849]
5. Hazra, A., Chatterjee, A. and Begley, T.P. Biosynthesis of the thiamin thiazole in Bacillus subtilis: identification of the product of the thiazole synthase-catalyzed reaction. J. Am. Chem. Soc. 131 (2009) 3225-3229. [PMID: 19216519]
6. Hazra, A.B., Han, Y., Chatterjee, A., Zhang, Y., Lai, R.Y., Ealick, S.E. and Begley, T.P. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J. Am. Chem. Soc. 133 (2011) 9311-9319. [PMID: 21534620]
*EC 2.8.1.11
Accepted name: molybdopterin synthase sulfurtransferase
Reaction: [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP + [cysteine desulfurase]-S-sulfanyl-L-cysteine + reduced acceptor = AMP + [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + [cysteine desulfurase] + oxidized acceptor
For diagram of reaction click here.
Other name(s): adenylyltransferase and sulfurtransferase MOCS3; Cnx5 (gene name); molybdopterin synthase sulfurylase
Systematic name: persulfurated L-cysteine desulfurase:[molybdopterin-synthase sulfur-carrier protein]-Gly-Gly sulfurtransferase
Comments: The enzyme transfers sulfur to form a thiocarboxylate moiety on the C-terminal glycine of the small subunit of EC 2.8.1.12, molybdopterin synthase. In the human, the reaction is catalysed by the rhodanese-like C-terminal domain (cf. EC 2.8.1.1) of the MOCS3 protein, a bifunctional protein that also contains EC 2.7.7.80, molybdopterin-synthase adenylyltransferase, at the N-terminal domain.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc
CAS registry number:
References:
1. Matthies, A., Nimtz, M. and Leimkuhler, S. Molybdenum cofactor biosynthesis in humans: identification of a persulfide group in the rhodanese-like domain of MOCS3 by mass spectrometry. Biochemistry 44 (2005) 7912-7920. [PMID: 15910006]
2. Leimkuhler, S. and Rajagopalan, K.V. A sulfurtransferase is required in the transfer of cysteine sulfur in the in vitro synthesis of molybdopterin from precursor Z in Escherichia coli. J. Biol. Chem. 276 (2001) 22024-22031. [PMID: 11290749]
3. Hanzelmann, P., Dahl, J.U., Kuper, J., Urban, A., Muller-Theissen, U., Leimkuhler, S. and Schindelin, H. Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains. Protein Sci. 18 (2009) 2480-2491. [PMID: 19798741]
4. Dahl, J.U., Urban, A., Bolte, A., Sriyabhaya, P., Donahue, J.L., Nimtz, M., Larson, T.J. and Leimkuhler, S. The identification of a novel protein involved in molybdenum cofactor biosynthesis in Escherichia coli. J. Biol. Chem. 286 (2011) 35801-35812. [PMID: 21856748]
EC 2.8.3.25
Accepted name: bile acid CoA-transferase
Reaction: (1) lithocholoyl-CoA + cholate = lithocholate + choloyl-CoA
Other name(s): baiF (gene name); baiK (gene name); bile acid coenzyme A transferase
Systematic name: lithocholoyl-CoA:cholate CoA-transferase
Comments: The enzyme, characterized from the gut bacterium Clostridium scindens, catalyses the last step in bile acid 7α-dehydroxylation, the removal of the CoA moiety from the products. By using a transferase rather than hydrolase, the bacteria conserve the thioester bond energy, saving ATP molecules. The enzyme has a broad substrate specificity and can use multiple acceptors, including allocholate, ursodeoxycholate, and β-muricholate.
References:
1. Ridlon, J.M. and Hylemon, P.B. Identification and characterization of two bile acid coenzyme A transferases from Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium. J. Lipid Res. 53 (2012) 66-76. [PMID: 22021638]
EC 3.1.1.100
Accepted name: chlorophyllide a hydrolase
Reaction: chlorophyllide a + H2O = 8-ethyl-12-methyl-3-vinyl-bacteriochlorophyllide d + methanol + CO2
Other name(s): bciC (gene name)
Systematic name: chlorophyllide-a hydrolase
Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), catalyses the first committed step in the biosynthesis of bacteriochlorophylls c, d and e, the removal of the C-132-methylcarboxyl group from chlorophyllide a. The reaction is very similar to the conversion of pheophorbide a to pyropheophorbide a during chlorophyll a degradation, which is catalysed by EC 3.1.1.82, pheophorbidase.
References:
1. Liu, Z. and Bryant, D.A. Identification of a gene essential for the first committed step in the biosynthesis of bacteriochlorophyll c. J. Biol. Chem. 286 (2011) 22393-22402. [PMID: 21550979]
EC 3.1.1.101
Accepted name: poly(ethylene terephthalate) hydrolase
Reaction: (ethylene terephthalate)n + H2O = (ethylene terephthalate)n-1 + ethylene terephthalate
Glossary: poly(ethylene terephthalate) = PET
Other name(s): PETase; PET hydrolase
Systematic name: poly(ethylene terephthalate) hydrolase
Comments: The enzyme, isolated from the bacterium Ideonella sakaiensis, also produces small amounts of terephthalate (cf. EC 3.1.1.102, mono(ethylene terephthalate) hydrolase). The reaction takes place on PET-film placed in solution.
References:
1. Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., Toyohara, K., Miyamoto, K., Kimura, Y. and Oda, K. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351 (2016) 1196-1199. [PMID: 26965627]
EC 3.1.1.102
Accepted name: mono(ethylene terephthalate) hydrolase
Reaction: ethylene terephthalate + H2O = terephthalate + ethylene glycol
Glossary: ethylene terephthalate = mono(ethylene terephthalate) = MHET = 4-[(2-hydroxyethoxy)carbonyl]benzoate
Other name(s): MHET hydrolase; MHETase
Systematic name: ethylene terephthalate acylhydrolase
Comments: The enzyme, isolated from the bacterium Ideonella sakaiensis, has no activity with poly(ethylene terephthalate) PET (cf. EC 3.1.1.101, poly(ethylene terephthalate) hydrolase).
References:
1. Yoshida, S., Hiraga, K., Takehana, T., Taniguchi, I., Yamaji, H., Maeda, Y., Toyohara, K., Miyamoto, K., Kimura, Y. and Oda, K. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351 (2016) 1196-1199. [PMID: 26965627]
[EC 3.1.2.26 Transferred entry: bile-acid-CoA hydrolase, now classified as EC 2.8.3.25, bile acid CoA transferase. (EC 3.1.2.26 created 2005, deleted 2016)]
EC 3.1.2.32
Accepted name: 2-aminobenzoylacetyl-CoA thioesterase
Reaction: 2-aminobenzoylacetyl-CoA + H2O = 2-aminobenzoylacetate + CoA
Other name(s): pqsE (gene name)
Systematic name: 2-aminobenzoylacetyl-CoA hydrolase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, participates in the production of the signal molecule 2-heptyl-4(1H)-quinolone (HHQ).
References:
1. Yu, S., Jensen, V., Seeliger, J., Feldmann, I., Weber, S., Schleicher, E., Haussler, S. and Blankenfeldt, W. Structure elucidation and preliminary assessment of hydrolase activity of PqsE, the Pseudomonas quinolone signal (PQS) response protein. Biochemistry 48 (2009) 10298-10307. [PMID: 19788310]
2. Drees, S.L. and Fetzner, S. PqsE of Pseudomonas aeruginosa acts as pathway-specific thioesterase in the biosynthesis of alkylquinolone signaling molecules. Chem. Biol. 22 (2015) 611-618. [PMID: 25960261]
[EC 3.1.3.13 Deleted entry: bisphosphoglycerate phosphatase. Recent studies have shown that this is a partial activity of EC 5.4.2.11, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) (EC 3.1.3.13 created 1961, deleted 2016)]
EC 3.1.3.103
Accepted name: 3-deoxy-D-glycero-D-galacto-nononate 9-phosphatase
Reaction: 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate + H2O = 3-deoxy-D-glycero-D-galacto-nononate + phosphate
Other name(s): 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase
Systematic name: 3-deoxy-D-glycero-D-galacto-nononate 9-phosphohydrolase
Comments: The enzyme, characterized from the bacterium Bacteroides thetaiotaomicron, is part of the biosynthesis pathway of the sialic acid 3-deoxy-D-glycero-D-galacto-nononate (KDN). KDN is abundant in extracellular glycoconjugates of lower vertebrates such as fish and amphibians, but is also found in the capsular polysaccharides of bacteria that belong to the Bacteroides genus.
References:
1. Wang, L., Lu, Z., Allen, K.N., Mariano, P.S. and Dunaway-Mariano, D. Human symbiont Bacteroides thetaiotaomicron synthesizes 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN). Chem. Biol. 15 (2008) 893-897. [PMID: 18804026]
2. Lu, Z., Wang, L., Dunaway-Mariano, D. and Allen, K.N. Structure-function analysis of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphatase defines specificity elements in type C0 haloalkanoate dehalogenase family members. J. Biol. Chem. 284 (2009) 1224-1233. [PMID: 18986982]
EC 3.1.3.104
Accepted name: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase
Reaction: 5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-(D-ribitylamino)uracil + phosphate
Other name(s): 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate phosphatase
Systematic name: 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphohydrolase
Comments: Requires Mg2+. The enzyme, which is found in plants and bacteria, is part of a pathway for riboflavin biosynthesis. Most forms of the enzyme has a broad substrate specificity [1,3].
References:
1. Haase, I., Sarge, S., Illarionov, B., Laudert, D., Hohmann, H.P., Bacher, A. and Fischer, M. Enzymes from the haloacid dehalogenase (HAD) superfamily catalyse the elusive dephosphorylation step of riboflavin biosynthesis. Chembiochem 14 (2013) 2272-2275. [PMID: 24123841]
2. London, N., Farelli, J.D., Brown, S.D., Liu, C., Huang, H., Korczynska, M., Al-Obaidi, N.F., Babbitt, P.C., Almo, S.C., Allen, K.N. and Shoichet, B.K. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry 54 (2015) 528-537. [PMID: 25513739]
3. Sarge, S., Haase, I., Illarionov, B., Laudert, D., Hohmann, H.P., Bacher, A. and Fischer, M. Catalysis of an essential step in vitamin B2 biosynthesis by a consortium of broad spectrum hydrolases. ChemBioChem 16 (2015) 2466-2469. [PMID: 26316208]
EC 3.2.1.197
Accepted name: β-1,2-mannosidase
Reaction: β-D-mannopyranosyl-(1→2)-β-D-mannopyranosyl-(1→2)-D-mannopyranose + H2O = β-D-mannopyranosyl-(1→2)-D-mannopyranose + α-D-mannopyranose
Systematic name: β-1,2-D-mannoside mannohydrolase
Comments: The enzyme, characterized from multiple bacterial species, catalyses the hydrolysis of terminal, non-reducing D-mannose residues from β-1,2-mannotriose and β-1,2-mannobiose. The mechanism involves anomeric inversion, resulting in the release of α-D-mannopyranose. Activity with β-1,2-mannotriose or higher oligosaccharides is higher than that with β-1,2-mannobiose.
References:
1. Cuskin, F., Basle, A., Ladeveze, S., Day, A.M., Gilbert, H.J., Davies, G.J., Potocki-Veronese, G. and Lowe, E.C. The GH130 family of mannoside phosphorylases contains glycoside hydrolases that target β-1,2-mannosidic linkages in Candida mannan. J. Biol. Chem. 290 (2015) 25023-25033. [PMID: 26286752]
2. Nihira, T., Chiku, K., Suzuki, E., Nishimoto, M., Fushinobu, S., Kitaoka, M., Ohtsubo, K. and Nakai, H. An inverting β-1,2-mannosidase belonging to glycoside hydrolase family 130 from Dyadobacter fermentans. FEBS Lett. 589 (2015) 3604-3610. [PMID: 26476324]
EC 3.2.1.198
Accepted name: α-mannan endo-1,2-α-mannanase
Reaction: Hydrolysis of the terminal α-D-mannosyl-(1→3)-α-D-mannose disaccharide from α-D-mannosyl-(1→3)-α-D-mannosyl-(1→2)-α-D-mannosyl-(1→2)-α-D-mannosyl side chains in fungal cell wall α-mannans.
Systematic name: α-mannan glucosylmannohydrolase
Comments: The enzyme, characterized from the gut bacteria Bacteroides thetaiotaomicron and Bacteroides xylanisolvens, can also catalyse the reaction of EC 3.2.1.130, glycoprotein endo-α-1,2-mannosidase.
References:
1. Hakki, Z., Thompson, A.J., Bellmaine, S., Speciale, G., Davies, G.J. and Williams, S.J. Structural and kinetic dissection of the endo-α-1,2-mannanase activity of bacterial GH99 glycoside hydrolases from Bacteroides spp. Chemistry 21 (2015) 1966-1977. [PMID: 25487964]
2. Cuskin, F., Lowe, E.C., Temple, M.J., Zhu, Y., Cameron, E.A., Pudlo, N.A., Porter, N.T., Urs, K., Thompson, A.J., Cartmell, A., Rogowski, A., Hamilton, B.S., Chen, R., Tolbert, T.J., Piens, K., Bracke, D., Vervecken, W., Hakki, Z., Speciale, G., Munoz-Munoz, J.L., Day, A., Pena, M.J., McLean, R., Suits, M.D., Boraston, A.B., Atherly, T., Ziemer, C.J., Williams, S.J., Davies, G.J., Abbott, D.W., Martens, E.C. and Gilbert, H.J. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517 (2015) 165-169. [PMID: 25567280]
EC 3.2.1.199
Accepted name: sulfoquinovosidase
Reaction: an α-sulfoquinovosyl diacylglycerol + H2O = sulfoquinovose + a 1,2-diacylglycerol
Other name(s): yihQ (gene name)
Systematic name: α-sulfoquinovosyl diacylglycerol sulfoquinovohydrolase
Comments: The enzyme, characterized from the bacteria Escherichia coli and Pseudomonas putida, hydrolyses terminal non-reducing α-sulfoquinovoside residues in α-sulfoquinovosyl diacylglycerides and α-sulfoquinovosyl glycerol.
References:
1. Shibuya, I. and Benson, A. A. Hydrolysis of α-sulphoquinovosides by β-galactosidase. Nature 192 (1961) 1186-1187.
2. Speciale, G., Jin, Y., Davies, G.J., Williams, S.J. and Goddard-Borger, E.D. YihQ is a sulfoquinovosidase that cleaves sulfoquinovosyl diacylglyceride sulfolipids. LID - 10.1038/nchembio.2023 [doi. Nat. Chem. Biol. (2016) . [PMID: 26878550]
[EC 3.3.2.5 Transferred entry: alkenylglycerophosphoethanolamine hydrolase, now included in EC 3.3.2.2, lysoplasmalogenase. (EC 3.3.2.5 created 1984, deleted 2016)]
EC 3.5.4.43
Accepted name: hydroxydechloroatrazine ethylaminohydrolase
Reaction: hydroxyatrazine + H2O = N-isopropylammelide + ethylamine
Glossary: hydroxyatrazine = 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine
Other name(s): atzB (gene name); 2,4-dihydroxy-6-(isopropylamino)-1,3,5-triazine ethylaminohydrolase
Systematic name: hydroxyatrazine ethylaminohydrolase
Comments: Contains Zn2+. This bacterial enzyme is involved indegradation of the herbicide atrazine. The enzyme has a broad substrate range, and requires a monohydroxylated s-triazine ring with a minimum of one primary or secondary amine substituent and either a chloride or amine leaving group. It catalyses both deamination and dechlorination reactions.
References:
1. Boundy-Mills, K.L., de Souza, M.L., Mandelbaum, R.T., Wackett, L.P. and Sadowsky, M.J. The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl. Environ. Microbiol. 63 (1997) 916-923. [PMID: 9055410]
2. Seffernick, J.L., Aleem, A., Osborne, J.P., Johnson, G., Sadowsky, M.J. and Wackett, L.P. Hydroxyatrazine N-ethylaminohydrolase (AtzB): an amidohydrolase superfamily enzyme catalyzing deamination and dechlorination. J. Bacteriol. 189 (2007) 6989-6997. [PMID: 17660279]
[EC 3.5.99.3 Transferred entry: hydroxydechloroatrazine ethylaminohydrolase, now classified as EC 3.5.4.43, hydroxydechloroatrazine ethylaminohydrolase (EC 3.5.99.3 created 2000, deleted 2016)] EC 4.1.1.103
Accepted name: γ-resorcylate decarboxylase
Reaction: 2,6-dihydroxybenzoate = 1,3-dihydroxybenzene + CO2
Glossary: 2,6-dihydroxybenzoate = γ-resorcylate
Other name(s): graF (gene name); tsdA (gene name)
Systematic name: 2,6-dihydroxybenzoate carboxy-lyase
Comments: The enzyme, characterized from several bacterial strains, is involved in the degradation of γ-resorcylate. It contains a zinc ion and a water molecule at the active site. The reaction is reversible, but equilibrium greatly favors the decarboxylation reaction.
References:
1. Yoshida, M., Fukuhara, N. and Oikawa, T. Thermophilic, reversible γ-resorcylate decarboxylase from Rhizobium sp. strain MTP-10005: purification, molecular characterization, and expression. J. Bacteriol. 186 (2004) 6855-6863. [PMID: 15466039]
2. Ishii, Y., Narimatsu, Y., Iwasaki, Y., Arai, N., Kino, K. and Kirimura, K. Reversible and nonoxidative γ-resorcylic acid decarboxylase: characterization and gene cloning of a novel enzyme catalyzing carboxylation of resorcinol, 1,3-dihydroxybenzene, from Rhizobium radiobacter. Biochem. Biophys. Res. Commun. 324 (2004) 611-620. [PMID: 15474471]
3. Matsui, T., Yoshida, T., Yoshimura, T. and Nagasawa, T. Regioselective carboxylation of 1,3-dihydroxybenzene by 2,6-dihydroxybenzoate decarboxylase of Pandoraea sp. 12B-2. Appl. Microbiol. Biotechnol. 73 (2006) 95-102. [PMID: 16683134]
4. Goto, M., Hayashi, H., Miyahara, I., Hirotsu, K., Yoshida, M. and Oikawa, T. Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (γ-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. J. Biol. Chem. 281 (2006) 34365-34373. [PMID: 16963440]
5. Kasai, D., Araki, N., Motoi, K., Yoshikawa, S., Iino, T., Imai, S., Masai, E. and Fukuda, M. γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 81 (2015) 7656-7665. [PMID: 26319878]
[EC 4.1.2.30 Transferred entry: 17α-hydroxyprogesterone aldolase. Now EC 1.14.14.32, 17α-hydroxyprogesterone deacetylase (EC 4.1.2.30 created 1976, deleted 2016)]
[EC 4.1.99.18 Transferred entry: cyclic pyranopterin phosphate synthase. Now known to be catalysed by the combined effort of EC 4.1.99.22, GTP 3,8-cyclase, and EC 4.6.1.17, cyclic pyranopterin monophosphate synthase (EC 4.1.99.18 created 2011, deleted 2016)]
*EC 4.1.99.20
Accepted name: 3-amino-4-hydroxybenzoate synthase
Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = 3-amino-4-hydroxybenzoate + phosphate + 2 H2O
For diagram of reaction click here.
Other name(s): 3,4-AHBA synthase; griH (gene name)
Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate hydro-lyase (cyclizing, 3-amino-4-hydroxybenzoate-forming)
Comments: Requires Mn2+ for maximum activity. The reaction is suggested to take place in several steps. Schiff base formation, double bond migration and dephosphorylation followed by ring opening and closing to form a pyrrolidine ring, and finally dehydration to form the product 3-amino-4-hydroxybenzoate. In the bacterium Streptomyces griseus the enzyme is involved in biosynthesis of grixazone, a yellow pigment that contains a phenoxazinone chromophore.
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EXPASY,
KEGG,
MetaCyc,
CAS registry number:
References:
1. Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944-36951. [PMID: 17003031]
EC 4.1.99.22
Accepted name: GTP 3',8-cyclase
Reaction: GTP + S-adenosyl-L-methionine + reduced electron acceptor = (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate + 5'-deoxyadenosine + L-methionine + oxidized electron acceptor
For diagram of reaction click here.
Other name(s): MOCS1A (gene name); moaA (gene name); cnx2 (gene name)
Systematic name: GTP 3',8-cyclase [(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate-forming]
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaA and Cnx2, respectively. In mammals it is catalysed by the MOCS1A domain of the bifunctional MOCS1 protein, which also catalyses EC 4.6.1.17, cyclic pyranopterin monophosphate synthase. The enzyme belongs to the superfamily of radical S-adenosyl-L-methionine (radical SAM) enzymes, and contains two oxygen-sensitive FeS clusters.
References:
1. Hänzelmann, P., Hernandez, H.L., Menzel, C., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Mendel, R.R. and Schindelin, H. Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. J. Biol. Chem. 279 (2004) 34721-34732. [PMID: 15180982]
2. Hänzelmann, P. and Schindelin, H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc. Natl. Acad. Sci. USA 101 (2004) 12870-12875. [PMID: 15317939]
3. Hänzelmann, P. and Schindelin, H. Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proc. Natl. Acad. Sci. USA 103 (2006) 6829-6834. [PMID: 16632608]
4. Lees, N.S., Hänzelmann, P., Hernandez, H.L., Subramanian, S., Schindelin, H., Johnson, M.K. and Hoffman, B.M. ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine-dependent enzyme MoaA: mechanistic implications. J. Am. Chem. Soc. 131 (2009) 9184-9185. [PMID: 19566093]
5. Hover, B.M., Loksztejn, A., Ribeiro, A.A. and Yokoyama, K. Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis. J. Am. Chem. Soc. 135 (2013) 7019-7032. [PMID: 23627491]
6. Hover, B.M. and Yokoyama, K. C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis. J. Am. Chem. Soc. 137 (2015) 3352-3359. [PMID: 25697423]
7. Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347-6352. [PMID: 25941396]
EC 4.2.1.168
Accepted name: GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
Reaction: GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + ammonia (overall reaction)
For diagram of reaction click here.
Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): colD (gene name)
Systematic name: GDP-4-dehydro-α-D-rhamnose 3-hydrolyase
Comments: This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5'-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.
References:
1. Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450-16460. [PMID: 15610039]
2. Cook, P.D. and Holden, H.M. A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation. Biochemistry 46 (2007) 14215-14224. [PMID: 17997582]
EC 4.2.3.156
Accepted name: hydroxysqualene synthase
Reaction: presqualene diphosphate + H2O = hydroxysqualene + diphosphate
For diagram of reaction click here.
Glossary: hydroxysqualene = (6E,10E,12R,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-12-ol
Other name(s): hpnC (gene name)
Systematic name: presqualene diphosphate diphosphate-lyase (adding water; hydroxyasqualene-forming)
Comments: This enzyme, isolated from the bacteria Rhodopseudomonas palustris and Zymomonas mobilis, participates, along with EC 2.5.1.103, presqualene diphosphate synthase, and EC 1.17.8.1, hydroxysqualene dehydroxylase, in the conversion of all-trans-farnesyl diphosphate to squalene. Eukaryotes achieve the same goal in a single step, catalysed by EC 2.5.1.21, squalene synthase.
References:
1. Pan, J.J., Solbiati, J.O., Ramamoorthy, G., Hillerich, B.S., Seidel, R.D., Cronan, J.E., Almo, S.C. and Poulter, C.D. Biosynthesis of squalene from farnesyl diphosphate in bacteria: three steps catalyzed by three enzymes. ACS Cent Sci 1 (2015) 77-82. [PMID: 26258173]
EC 4.4.1.34
Accepted name: isoprene-epoxide—glutathione S-transferase
Reaction: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol = (3R)-3,4-epoxy-3-methylbut-1-ene + glutathione
For diagram of reaction click here.
Other name(s): isoI (gene name)
Systematic name: 2-(glutathion-S-yl)-2-methylbut-3-en-1-ol lyase [(3R)-3,4-epoxy-3-methylbut-1-ene forming]
Comments: The enzyme, characterized from the bacterium Rhodococcus sp. AD45, is involved in isoprene degradation. The enzyme can catalyse the glutathione-dependent ring opening of various epoxides, but the highest activity is with (3R)-3,4-epoxy-3-methylbut-1-ene, which is derived from isoprene by EC 1.14.13.69, alkene monooxygenase.
References:
1. van Hylckama Vlieg, J.E., Kingma, J., van den Wijngaard, A.J. and Janssen, D.B. A glutathione S-transferase with activity towards cis-1, 2-dichloroepoxyethane is involved in isoprene utilization by Rhodococcus sp. strain AD45. Appl. Environ. Microbiol. 64 (1998) 2800-2805. [PMID: 9687433]
2. van Hylckama Vlieg, J.E., Kingma, J., Kruizinga, W. and Janssen, D.B. Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J. Bacteriol. 181 (1999) 2094-2101. [PMID: 10094686]
EC 4.6.1.17
Accepted name: cyclic pyranopterin monophosphate synthase
Reaction: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
For diagram of reaction click here.
Other name(s): MOCS1B (gene name); moaC (gene name); cnx3 (gene name)
Systematic name: (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate lyase (cyclic pyranopterin phosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). In bacteria and plants the reaction is catalysed by MoaC and Cnx3, respectively. In mammals the reaction is catalysed by the MOCS1B domain of the bifuctional MOCS1 protein, which also catalyses EC 4.1.99.22, GTP 3',8-cyclase.
References:
1. Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24-36. [PMID: 9692897]
2. Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082-1087. [PMID: 7836363]
3. Hover, B.M., Tonthat, N.K., Schumacher, M.A. and Yokoyama, K. Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis. Proc. Natl. Acad. Sci. USA 112 (2015) 6347-6352. [PMID: 25941396]
*EC 4.99.1.1
Accepted name: protoporphyrin ferrochelatase
Reaction: protoheme + 2 H+ = protoporphyrin + Fe2+
For diagram of reaction click here.
Other name(s): ferro-protoporphyrin chelatase; iron chelatase (ambiguous); heme synthetase (ambiguous); heme synthase (ambiguous); protoheme ferro-lyase; ferrochelatase (ambiguous)
Systematic name: protoheme ferro-lyase (protoporphyrin-forming)
Comments: The enzyme catalyses the terminal step in the heme biosynthesis pathways of eukaryotes and Gram-negative bacteria.
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CAS registry number: 9012-93-5
References:
1. Bloomer, J.R., Hill, H.D., Morton, K.O., Anderson-Burnham, L.A. and Straka, J.G. The enzyme defect in bovine protoporphyria. Studies with purified ferrochelatase. J. Biol. Chem. 262 (1987) 667-671. [PMID: 3805002]
2. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 1. Assay and properties of ferrochelatase from a pig-liver mitochondrial extract. Biochem. J. 87 (1963) 181-185. [PMID: 13972328]
3. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 2. An investigation of the role of ferrochelatase in the biosynthesis of various haem prosthetic groups. Biochem. J. 87 (1963) 186-192. [PMID: 13972329]
*EC 6.2.1.19
Accepted name: long-chain-fatty-acid—protein ligase
Reaction: ATP + a long-chain fatty acid + [protein]-L-cysteine = AMP + diphosphate + a [protein]-S-(long-chain-acyl)-L-cysteine
Other name(s): luxE (gene name); acyl-protein synthetase; long-chain-fatty-acid—luciferin-component ligase
Systematic name: long-chain-fatty-acid:protein ligase (AMP-forming)
Comments: Together with a transferase component (EC 3.1.2.2/EC 3.1.2.14) and a reductase component (EC 1.2.1.50), this enzyme forms a multienzyme fatty acid reductase complex that produces the long-chain aldehyde substrate of the bacterial luciferase enzyme (EC 1.14.14.3). The enzyme activates free long-chain fatty acids, generated by the action of the transferase component, forming a fatty acyl-AMP intermediate, followed by the transfer of the acyl group to an internal L-cysteine residue. It then transfers the acyl group to EC 1.2.1.50, long-chain acyl-protein thioester reductase.
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CAS registry number: 82657-98-5
References:
1. Riendeau, D., Rodrigues, A. and Meighen, E. Resolution of the fatty acid reductase from Photobacterium phosphoreum into acyl protein synthetase and acyl-CoA reductase activities. Evidence for an enzyme complex. J. Biol. Chem. 257 (1982) 6908-6915. [PMID: 7085612]
2. Rodriguez, A. and Meighen, E. Fatty acyl-AMP as an intermediate in fatty acid reduction to aldehyde in luminescent bacteria. J. Biol. Chem. 260 (1985) 771-774. [PMID: 3968067]
3. Wall, L. and Meighen, E.A. Subunit structure of the fatty-acid reductase complex from Photobacterium phosphoreum. Biochemistry 25 (1986) 4315-4321.
4. Soly, R.R. and Meighen, E.A. Identification of the acyl transfer site of fatty acyl-protein synthetase from bioluminescent bacteria. J. Mol. Biol. 219 (1991) 69-77. [PMID: 2023262]
5. Lin, J.W., Chao, Y.F. and Weng, S.F. Nucleotide sequence and functional analysis of the luxE gene encoding acyl-protein synthetase of the lux operon from Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 228 (1996) 764-773. [PMID: 8941351]
EC 6.2.1.47
Accepted name: medium-chain-fatty-acid—[acyl-carrier-protein] ligase
Reaction: ATP + a medium-chain fatty acid + a holo-[acyl-carrier protein] = AMP + diphosphate + a medium-chain acyl-[acyl-carrier protein]
Other name(s): jamA (gene name)
Systematic name: medium-chain-fatty-acid:[acyl-carrier protein] ligase (AMP-forming)
Comments: The enzyme ligates medium chain fatty acids (with aliphatic chain of 6-12 carbons) to an acyl-carrier protein.
References:
1. Edwards, D.J., Marquez, B.L., Nogle, L.M., McPhail, K., Goeger, D.E., Roberts, M.A. and Gerwick, W.H. Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. Chem. Biol. 11 (2004) 817-833. [PMID: 15217615]
2. Zhu, X., Liu, J. and Zhang, W. De novo biosynthesis of terminal alkyne-labeled natural products. Nat. Chem. Biol. 11 (2015) 115-120. [PMID: 25531891]
*EC 6.3.1.2
Accepted name: glutamine synthetase
Reaction: ATP + L-glutamate + NH3 = ADP + phosphate + L-glutamine
Other name(s): glutamate—ammonia ligase; glutamylhydroxamic synthetase; L-glutamine synthetase; GS
Systematic name: L-glutamate:ammonia ligase (ADP-forming)
Comments: Glutamine synthetase, which catalyses the incorporation of ammonium into glutamate, is a key enzyme of nitrogen metabolism found in all domains of life. Several types have been described, differing in their oligomeric structures and cofactor requirements.
Links to other databases:
BRENDA,
EXPASY,
GTD,
KEGG,
MetaCyc,
PDB,
CAS registry number: 9023-70-5
References:
1. Elliott, W.H. Isolation of glutamine synthetase and glutamotransferase from green peas. J. Biol. Chem. 201 (1953) 661-672. [PMID: 13061404]
2. Fry, B.A. Glutamine synthesis by Micrococcus pyogenes var. aureus. Biochem. J. 59 (1955) 579-589. [PMID: 14363150]
3. Lajtha, A., Mela, P. and Waelsch, H. Manganese-dependent glutamotransferase. J. Biol. Chem. 205 (1953) 553-564. [PMID: 13129232]
4. Meister, A. Glutamine synthesis. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 6, Academic Press, New York, 1962, pp. 443-468.
5. Woolfolk, C.A., Shapiro, B. and Stadtman, E.R. Regulation of glutamine synthetase. I. Purification and properties of glutamine synthetase from Escherichia coli. Arch. Biochem. Biophys. 116 (1966) 177-192. [PMID: 5336023]
6. Kumada, Y., Benson, D.R., Hillemann, D., Hosted, T.J., Rochefort, D.A., Thompson, C.J., Wohlleben, W. and Tateno, Y. Evolution of the glutamine synthetase gene, one of the oldest existing and functioning genes. Proc. Natl. Acad. Sci. USA 90 (1993) 3009-3013. [PMID: 8096645]
7. Llorca, O., Betti, M., Gonzalez, J.M., Valencia, A., Marquez, A.J. and Valpuesta, J.M. The three-dimensional structure of an eukaryotic glutamine synthetase: functional implications of its oligomeric structure. J. Struct. Biol. 156 (2006) 469-479. [PMID: 16884924]
8. Martinez-Espinosa, R.M., Esclapez, J., Bautista, V. and Bonete, M.J. An octameric prokaryotic glutamine synthetase from the haloarchaeon Haloferax mediterranei. FEMS Microbiol. Lett. 264 (2006) 110-116. [PMID: 17020556]
*EC 6.5.1.1
Accepted name: DNA ligase (ATP)
Reaction: ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate (overall reaction)
Other name(s): polydeoxyribonucleotide synthase (ATP); polynucleotide ligase (ambiguous); sealase; DNA repair enzyme (ambiguous); DNA joinase (ambiguous); DNA ligase (ambiguous); deoxyribonucleic ligase (ambiguous); deoxyribonucleate ligase (ambiguous); DNA-joining enzyme (ambiguous); deoxyribonucleic-joining enzyme (ambiguous); deoxyribonucleic acid-joining enzyme (ambiguous); deoxyribonucleic repair enzyme (ambiguous); deoxyribonucleic joinase (ambiguous); deoxyribonucleic acid ligase (ambiguous); deoxyribonucleic acid joinase (ambiguous); deoxyribonucleic acid repair enzyme (ambiguous); poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)
Systematic name: poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)
Comments: The enzyme catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. RNA can also act as substrate, to some extent. cf. EC 6.5.1.2, DNA ligase (NAD+), EC 6.5.1.6, DNA ligase (ATP or NAD+), and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
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CAS registry number: 9015-85-4
References:
1. Becker, A., Lyn, G., Gefter, M. and Hurwitz, J. The enzymatic repair of DNA. II. Characterization of phage-induced sealase. Proc. Natl. Acad. Sci. USA 58 (1967) 1996-2003. [PMID: 4295584]
2. Bertazzoni, U., Mathelet, M. and Campagnari, F. Purification and properties of a polynucleotide ligase from calf thymus glands. Biochim. Biophys. Acta 287 (1972) 404-414. [PMID: 4641251]
3. Weiss, B. and Richardson, C.C. Enzymatic breakage and joining of deoxyribonucleic acid. I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. USA 57 (1967) 1021-1028. [PMID: 5340583]
4. Howes, T.R. and Tomkinson, A.E. DNA ligase I, the replicative DNA ligase. Subcell. Biochem. 62 (2012) 327-341. [PMID: 22918593]
*EC 6.5.1.3
Accepted name: RNA ligase (ATP)
Reaction: ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate (overall reaction)
Other name(s): polyribonucleotide synthase (ATP); RNA ligase; polyribonucleotide ligase; ribonucleic ligase; poly(ribonucleotide):poly(ribonucleotide) ligase (AMP-forming)
Systematic name: poly(ribonucleotide)-3'-hydroxyl:5'-phospho-poly(ribonucleotide) ligase (ATP)
Comments: The enzyme catalyses the ligation of RNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in RNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[RNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
MetaCyc,
PDB,
CAS registry number: 37353-39-2
References:
1. Silber, R., Malathi, V.G. and Hurwitz, J. Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. USA 69 (1972) 3009-3013. [PMID: 4342972]
2. Cranston, J.W., Silber, R., Malathi, V.G. and Hurwitz, J. Studies on ribonucleic acid ligase. Characterization of an adenosine triphosphate-inorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme. J. Biol. Chem. 249 (1974) 7447-7456. [PMID: 4373468]
3. Sugino, A., Snoper, T.J. and Cozzarelli, N.R. Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates. J. Biol. Chem. 252 (1977) 1732-1738. [PMID: 320212]
4. Romaniuk, P.J. and Uhlenbeck, O.C. Joining of RNA molecules with RNA ligase. Methods Enzymol. 100 (1983) 52-59. [PMID: 6194411]
5. Ho, C.K., Wang, L.K., Lima, C.D. and Shuman, S. Structure and mechanism of RNA ligase. Structure 12 (2004) 327-339. [PMID: 14962393]
6. Nandakumar, J., Shuman, S. and Lima, C.D. RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. Cell 127 (2006) 71-84. [PMID: 17018278]
(2) a (2S,3S)-flavan-3-ol + 2 NADP+ = an anthocyanidin with a 3-hydroxy group + 2 NADPH + H+
protoviolaceinate = 5-(5-hydroxy-1H-indol-3-yl)-3-(1H-indol-3-yl)-1H-pyrrole-2-carboxylate
(1a) aurachin C + NAD(P)H + H+ + O2 = 2-hydroxy-1a-methyl-7a-[(2E,6E)-farnesyl]-1a,2-dihydrooxireno[2,3-b]quinolin-7(7aH)-one + NAD(P)+ + H2O
(1b) 2-hydroxy-1a-methyl-7a-[(2E,6E)-farnesyl]-1a,2-dihydrooxireno[2,3-b]quinolin-7(7aH)-one = 4-hydroxy-2-methyl-3-oxo-4-[(2E,6E)-farnesyl]-3,4-dihydroquinoline 1-oxide
2-hydroxy-1a-methyl-7a-[(2E,6E)-farnesyl]-1a,2-dihydrooxireno[2,3-b]quinolin-7(7aH)-one = 2-hydroxy-1a-methyl-7a-((2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl)-1a,2-dihydrooxireno[2,3-b]quinolin-7(7aH)-one
4-hydroxy-2-methyl-3-oxo-4-[(2E,6E)-farnesyl]-3,4-dihydroquinoline 1-oxide = 4-hydroxy-2-methyl-4-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]quinolin-3(4H)-one 1-oxide
aurachin B = 2-methyl-4-[(2E,6E)-farnesyl]-3-quinolinol 1-oxide
(2) protodeoxyviolaceinate + NAD(P)H + O2 = deoxyviolaceinate + NAD(P)+ H2O
(2) 2-methylpropanamine + FMNH2 + O2 = N-(2-methylpropanoyl)hydroxylamine + FMN + H2O
ipsdienol = 2-methyl-6-methyleneocta-2,7-dien-4-ol
(2) 17α-hydroxypregnenolone + [reduced NADPH—hemoprotein reductase] + O2 = 3β-hydroxyandrost-5-en-17-one + acetate + [oxidized NADPH—hemoprotein reductase] + H2
(2) ATP + validone = ADP + validone 7-phosphate
validone = (2R,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexan-1-one
(2) ATP + 19-(4-hydroxyphenyl)nonadecanoate = diphosphate + 19-(4-hydroxyphenyl)nonadecanoyl adenylate
(2) deoxycholoyl-CoA + cholate = deoxycholate + choloyl-CoA
ethylene terephthalate = 4-[(2-hydroxyethoxy)carbonyl]benzoate
N-isopropylammelide = 2,4-dihydroxy-6-(isopropylamino)-1,3,5-triazine
1,3-dihydroxybenzene = resorcinol
(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-(2S,3S,6R)-3-hydroxy-5-amino-6-methyl-3,6-dihydro-2H-pyran + 2-oxoglutarate + H2O
(1b) GDP-(2S,3S,6R)-3-hydroxy-5-amino-6-methyl-3,6-dihydro-2H-pyran = GDP-(2S,3S,6R)-3-hydroxy-5-imino-6-methyloxane (spontaneous)
(1c) GDP-(2S,3S,6R)-3-hydroxy-5-imino-6-methyloxane + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + ammonia (spontaneous)
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
(1b) [DNA ligase]-N6-(5'-adenylyl)-L-lysine + 5'-phospho-(deoxyribonucleotide)m = 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m + [DNA ligase]-L-lysine
(1c) (deoxyribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N6-(5'-adenylyl)-L-lysine + diphosphate
(1b) [RNA ligase]-N6-(5'-adenylyl)-L-lysine + 5'-phospho-(ribonucleotide)m = 5'-(5'-diphosphoadenosine)-(ribonucleotide)m + [RNA ligase]-L-lysine
(1c) (ribonucleotide)n-3'-hydroxyl + 5'-(5'-diphosphoadenosine)-(ribonucleotide)m = (ribonucleotide)n+m + AMP
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