Accepted name: L-galactose 1-dehydrogenase
Reaction: L-galactose + NAD+ = L-galactono-1,4-lactone + NADH + H+
Other name(s): L-GalDH; L-galactose dehydrogenase
Systematic name: L-galactose:NAD+ 1-oxidoreductase
Comments: The enzyme catalyses a step in the ascorbate biosynthesis in higher plants (Smirnoff-Wheeler pathway). The activity with NADP+ is less than 10% of the activity with NAD+.
References:
1. Mieda, T., Yabuta, Y., Rapolu, M., Motoki, T., Takeda, T., Yoshimura, K., Ishikawa, T. and Shigeoka, S. Feedback inhibition of spinach L-galactose dehydrogenase by L-ascorbate. Plant Cell Physiol. 45 (2004) 1271-1279. [PMID: 15509850]
2. Gatzek, S., Wheeler, G.L. and Smirnoff, N. Antisense suppression of L-galactose dehydrogenase in Arabidopsis thaliana provides evidence for its role in ascorbate synthesis and reveals light modulated L-galactose synthesis. Plant J. 30 (2002) 541-553. [PMID: 12047629]
3. Wheeler, G.L., Jones, M.A. and Smirnoff, N. The biosynthetic pathway of vitamin C in higher plants. Nature 393 (1998) 365-369. [PMID: 9620799]
4. Oh, M.M., Carey, E.E. and Rajashekar, C.B. Environmental stresses induce health-promoting phytochemicals in lettuce. Plant Physiol. Biochem. 47 (2009) 578-583. [PMID: 19297184]
EC 1.1.1.317
Accepted name: perakine reductase
Reaction: raucaffrinoline + NADP+ = perakine + NADPH + H+
For diagram of reaction click here
Glossary: raucaffrinoline = (17R,20α,21β)-1,2-didehydro-1-demethyl-19-hydroxy-21-methyl-18-norajmalan-17-yl acetate
Systematic name: raucaffrinoline:NADP+ oxidoreductase
Comments: The biosynthesis of raucaffrinoline from perakine is a side route of the ajmaline biosynthesis pathway. The enzyme is a member of the aldo-keto reductase enzyme superfamily from higher plants.
References:
1. Sun, L., Ruppert, M., Sheludko, Y., Warzecha, H., Zhao, Y. and Stockigt, J. Purification, cloning, functional expression and characterization of perakine reductase: the first example from the AKR enzyme family, extending the alkaloidal network of the plant Rauvolfia. Plant Mol. Biol. 67 (2008) 455-467. [PMID: 18409028]
2. Rosenthal, C., Mueller, U., Panjikar, S., Sun, L., Ruppert, M., Zhao, Y. and Stockigt, J. Expression, purification, crystallization and preliminary X-ray analysis of perakine reductase, a new member of the aldo-keto reductase enzyme superfamily from higher plants. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 1286-1289. [PMID: 17142919]
EC 1.1.3.42
Accepted name: prosolanapyrone-II oxidase
Reaction: prosolanapyrone II + O2 = prosolanapyrone III + H2O2
For diagram of reaction click here
Glossary: prosolanapyrone II = 3-(hydroxymethyl)-4-methoxy-6-(1E,7E,9E)-undeca-1,7,9-trien-1-yl-2H-pyran-2-one
Other name(s): Sol5 (ambiguous); SPS (ambiguous); solanapyrone synthase (bifunctional enzyme: prosolanapyrone II oxidase/prosolanapyrone III cycloisomerase); prosolanapyrone II oxidase
Systematic name: prosolanapyrone-II:oxygen 3'-oxidoreductase
Comments: The enzyme is involved in the biosynthesis of the phytotoxin solanapyrone by some fungi. The bifunctional enzyme catalyses the oxidation of prosolanapyrone II and the subsequent Diels Alder cycloisomerization of the product prosolanapyrone III to (–)-solanapyrone A (cf. EC 5.5.1.20, prosolanapyrone III cycloisomerase).
References:
1. Kasahara, K., Miyamoto, T., Fujimoto, T., Oguri, H., Tokiwano, T., Oikawa, H., Ebizuka, Y. and Fujii, I. Solanapyrone synthase, a possible Diels-Alderase and iterative type I polyketide synthase encoded in a biosynthetic gene cluster from Alternaria solani. Chembiochem. 11 (2010) 1245-1252. [PMID: 20486243]
2. Katayama, K., Kobayashi, T., Oikawa, H., Honma, M. and Ichihara, A. Enzymatic activity and partial purification of solanapyrone synthase: first enzyme catalyzing Diels-Alder reaction. Biochim. Biophys. Acta 1384 (1998) 387-395. [PMID: 9659400]
3. Katayama, K., Kobayashi, T., Chijimatsu, M., Ichihara, A. and Oikawa, H. Purification and N-terminal amino acid sequence of solanapyrone synthase, a natural Diels-Alderase from Alternaria solani. Biosci. Biotechnol. Biochem. 72 (2008) 604-607. [PMID: 18256508]
EC 1.1.9 With a copper protein as acceptor
EC 1.1.9.1
Accepted name: alcohol dehydrogenase (azurin)
Reaction: a primary alcohol + azurin = an aldehyde + reduced azurin
Other name(s): type II quinoprotein alcohol dehydrogenase; quinohaemoprotein ethanol dehydrogenase; QHEDH; ADHIIB
Systematic name: alcohol:azurin oxidoreductase
Comments: A soluble, periplasmic PQQ-containing quinohaemoprotein. Also contains a single haem c. Occurs in Comamonas and Pseudomonas. Does not require an amine activator. Oxidizes a wide range of primary and secondary alcohols, and also aldehydes and large substrates such as sterols; methanol is not a substrate. Usually assayed with phenazine methosulfate or ferricyanide. Like all other quinoprotein alcohol dehydrogenases it has an 8-bladed 'propeller' structure, a calcium ion bound to the PQQ in the active site and an unusual disulfide ring structure in close proximity to the PQQ.
References:
1. Groen, B.W., van Kleef, M.A. and Duine, J.A. Quinohaemoprotein alcohol dehydrogenase apoenzyme from Pseudomonas testosteroni. Biochem. J. 234 (1986) 611-615. [PMID: 3521592]
2. de Jong, G.A., Caldeira, J., Sun, J., Jongejan, J.A., de Vries, S., Loehr, T.M., Moura, I., Moura, J.J. and Duine, J.A. Characterization of the interaction between PQQ and heme c in the quinohemoprotein ethanol dehydrogenase from Comamonas testosteroni. Biochemistry 34 (1995) 9451-9458. [PMID: 7626615]
3. Toyama, H., Fujii, A., Matsushita, K., Shinagawa, E., Ameyama, M. and Adachi, O. Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols. J. Bacteriol. 177 (1995) 2442-2450. [PMID: 7730276]
4. Matsushita, K., Yamashita, T., Aoki, N., Toyama, H. and Adachi, O. Electron transfer from quinohemoprotein alcohol dehydrogenase to blue copper protein azurin in the alcohol oxidase respiratory chain of Pseudomonas putida HK5. Biochemistry 38 (1999) 6111-6118. [PMID: 10320337]
5. Chen, Z.W., Matsushita, K., Yamashita, T., Fujii, T.A., Toyama, H., Adachi, O., Bellamy, H.D. and Mathews, F.S. Structure at 1.9 Å resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5. Structure 10 (2002) 837-849. [PMID: 12057198]
6. Oubrie, A., Rozeboom, H.J., Kalk, K.H., Huizinga, E.G. and Dijkstra, B.W. Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer. J. Biol. Chem. 277 (2002) 3727-3732. [PMID: 11714714]
[EC 1.1.98.1 Transferred entry: Now EC 1.1.9.1 alcohol dehydrogenase (azurin) (EC 1.1.98.1 created 2010, deleted 2011)]
*EC 1.3.8.2
Accepted name: 4,4'-diapophytoene desaturase
Reaction: 15-cis-4,4'-diapophytoene + 4 FAD = all-trans-4,4'-diapolycopene + 4 FADH2 (overall reaction)
For diagram of reaction click here
Other name(s): dehydrosqualene desaturase; CrtN; 4,4'-diapophytoene:FAD oxidoreductase
Systematic name: 15-cis-4,4'-diapophytoene:FAD oxidoreductase
Comments: Typical of Staphylococcus aureus and some other bacteria such as Heliobacillus sp. Responsible for four successive dehydrogenations. In some species it only proceeds as far as all-trans-4,4'-diaponeurosporene.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
References:
1. Wieland, B., Feil, C., Gloria-Maercker, E., Thumm, G., Lechner, M., Bravo, J.M., Poralla, K. and Gotz, F. Genetic and biochemical analyses of the biosynthesis of the yellow carotenoid 4,4'-diaponeurosporene of Staphylococcus aureus. J. Bacteriol. 176 (1994) 7719-7726. [PMID: 8002598]
2. Raisig, A. and Sandmann, G. 4,4'-diapophytoene desaturase: catalytic properties of an enzyme from the C30 carotenoid pathway of Staphylococcus aureus. J. Bacteriol. 181 (1999) 6184-6187. [PMID: 10498735]
3. Raisig, A. and Sandmann, G. Functional properties of diapophytoene and related desaturases of C30 to C40 carotenoid biosynthetic pathways. Biochim. Biophys. Acta 1533 (2001) 164-170. [PMID: 11566453]
EC 1.10.9 With a copper protein as acceptor
EC 1.10.9.1
Accepted name: plastoquinol—plastocyanin reductase
Reaction: plastoquinol-1 + 2 oxidized plastocyanin + 2 H+[side 1] = plastoquinone + 2 reduced plastocyanin + 2 H+[side 2]
Other name(s): plastoquinol/plastocyanin oxidoreductase; cytochrome b6/f complex; cytochrome b6/ complex
Systematic name: plastoquinol:oxidized-plastocyanin oxidoreductase
Comments: Contains two b-type cytochromes, two c-type cytochromes (cn and f), and a [2Fe-2S] Rieske cluster. Cytochrome c-552 can act as acceptor instead of plastocyanin, but more slowly. In chloroplasts, protons are translocated through the thylakoid membrane from the lumen to the stroma.
References:
1. Hurt, E. and Hauska, G. A cytochrome f/b6 complex of five polypeptides with plastoquinol-plastocyanin-oxidoreductase activity from spinach chloroplasts. Eur. J. Biochem. 117 (1981) 591-595. [PMID: 6269845]
2. Cramer, W.A. and Zhang, H. Consequences of the structure of the cytochrome b6f complex for its charge transfer pathways. Biochim. Biophys. Acta 1757 (2006) 339-345. [PMID: 16787635]
[EC 1.10.99.1 Transferred entry: Now EC 1.10.9.1 plastoquinol—plastocyanin reductase (EC 1.10.99.1 created 1984, deleted 2011)]
[EC 1.13.11.44 Deleted entry: linoleate diol synthase. Activity is covered by EC 1.13.11.60, linoleate 8R-lipoxygenase and EC 5.4.4.6, 9,12-octadecadienoate 8-hydroperoxide 8S-isomerase. (EC 1.13.11.44 created 2000, deleted 2011)]
EC 1.13.11.60
Accepted name: linoleate 8R-lipoxygenase
Reaction: linoleate + O2 = (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate
Glossary: linoleate = (9Z,12Z)-octadeca-9,12-dienoate
Other name(s): linoleic acid 8R-dioxygenase; 5,8-LDS (bifunctional enzyme); 7,8-LDS (bifunctional enzyme); 5,8-linoleate diol synthase (bifunctional enzyme); 7,8-linoleate diol synthase (bifunktional enzyme); PpoA
Systematic name: linoleate:oxygen (8R)-oxidoreductase
Comments: The enzyme contains heme [1,4]. The bifunctional enzyme from Aspergillus nidulans uses different heme domains to catalyse two separate reactions. Linoleic acid is oxidized within the N-terminal heme peroxidase domain to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate, which is subsequently isomerized by the C-terminal P450 heme thiolate domain to (5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate (cf. EC 5.4.4.5, 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase) [1]. The bifunctional enzyme from Gaeumannomyces graminis also catalyses the oxidation of linoleic acid to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate, but its second domain isomerizes it to (7S,8S,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate (cf. EC 5.4.4.6, 9,12-octadecadienoate 8-hydroperoxide 8S-isomerase) [4].
References:
1. Brodhun, F., Gobel, C., Hornung, E. and Feussner, I. Identification of PpoA from Aspergillus nidulans as a fusion protein of a fatty acid heme dioxygenase/peroxidase and a cytochrome P450. J. Biol. Chem. 284 (2009) 11792-11805. [PMID: 19286665]
2. Hamberg, M., Zhang, L.-Y., Brodowsky, I.D. and Oliw, E.H. Sequential oxygenation of linoleic acid in the fungus Gaeumannomyces graminis: stereochemistry of dioxygenase and hydroperoxide isomerase reactions. Arch. Biochem. Biophys. 309 (1994) 77-80. [PMID: 8117115]
3. Garscha, U. and Oliw, E. Pichia expression and mutagenesis of 7,8-linoleate diol synthase change the dioxygenase and hydroperoxide isomerase. Biochem. Biophys. Res. Commun. 373 (2008) 579-583. [PMID: 18586008]
4. Su, C. and Oliw, E.H. Purification and characterization of linoleate 8-dioxygenase from the fungus Gaeumannomyces graminis as a novel hemoprotein. J. Biol. Chem. 271 (1996) 14112-14118. [PMID: 8662736]
EC 1.13.11.61
Accepted name: linolenate 9R-lipoxygenase
Reaction: α-linolenate + O2 = (9R,10E,12Z,15Z)-9-hydroperoxyoctadeca-10,12,15-trienoate
Glossary: linoleate = (9Z,12Z)-octadeca-9,12-dienoate
Other name(s): NspLOX; (9R)-LOX; linoleate 9R-dioxygenase
Systematic name: α-linolenate:oxygen (9R)-oxidoreductase
Comments: In cyanobacteria the enzyme is involved in oxylipin biosynthesis. The enzyme also converts linoleate to (9R,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate.
References:
1. Jerneren, F., Hoffmann, I. and Oliw, E.H. Linoleate 9R-dioxygenase and allene oxide synthase activities of Aspergillus terreus. Arch. Biochem. Biophys. 495 (2010) 67-73. [PMID: 20043865]
2. Andreou, A.Z., Vanko, M., Bezakova, L. and Feussner, I. Properties of a mini 9R-lipoxygenase from Nostoc sp. PCC 7120 and its mutant forms. Phytochemistry 69 (2008) 1832-1837. [PMID: 18439634]
3. Lang, I., Gobel, C., Porzel, A., Heilmann, I. and Feussner, I. A lipoxygenase with linoleate diol synthase activity from Nostoc sp. PCC 7120. Biochem. J. 410 (2008) 347-357. [PMID: 18031288]
EC 1.13.11.62
Accepted name: linoleate 10R-lipoxygenase
Reaction: linoleate + O2 = (8E,10R,12Z)-10-hydroperoxyoctadeca-8,12-dienoate
Glossary: linoleate = (9Z,12Z)-octadeca-9,12-dienoate
Other name(s): 10R-DOX; (10R)-dioxygenase; 10R-dioxygenase
Systematic name: linoleate:oxygen (10R)-oxidoreductase
Comments: The enzyme is involved in biosynthesis of oxylipins, which affect sporulation, development, and pathogenicity of Aspergillus spp.
References:
1. Garscha, U. and Oliw, E.H. Leucine/valine residues direct oxygenation of linoleic acid by (10R)- and (8R)-dioxygenases: expression and site-directed mutagenesis of (10R)-dioxygenase with epoxyalcohol synthase activity. J. Biol. Chem. 284 (2009) 13755-13765. [PMID: 19289462]
2. Jerneren, F., Garscha, U., Hoffmann, I., Hamberg, M. and Oliw, E.H. Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus. Biochim. Biophys. Acta 1801 (2010) 503-507. [PMID: 20045744]
EC 1.14.13.133
Accepted name: pentalenene oxygenase
Reaction: pentalenene + 2 NADPH + 2 H+ + 2 O2 = pentalen-13-al + 2 NADP+ + 3 H2O (overall reaction)
For diagram of reaction click here.
Other name(s): PtlI
Systematic name: pentalenene,NADPH:oxygen 13-oxidoreductase
Comments: A heme-thiolate protein (P-450). The enzyme is involved in the biosynthesis of pentalenolactone and related antibiotics.
References:
1. Quaderer, R., Omura, S., Ikeda, H. and Cane, D.E. Pentalenolactone biosynthesis. Molecular cloning and assignment of biochemical function to PtlI, a cytochrome P450 of Streptomyces avermitilis. J. Am. Chem. Soc. 128 (2006) 13036-13037. [PMID: 17017767]
EC 1.14.13.134
Accepted name: β-amyrin 11-oxidase
Reaction: β-amyrin + 2 O2 + 2 NADPH + 2 H+ = 11-oxo-β-amyrin + 3 H2O + 2 NADP+ (overall reaction)
For diagram of reaction click here.
Other name(s): CYP88D6
Systematic name: β-amyrin,NADPH:oxygen oxidoreductase (hydroxylating)
Comments: Requires cytochrome P450. Part of the glycyrrhizin biosynthesis pathway. The enzyme is also able to oxidize 30-hydroxy-β-amyrin to 11α,30-dihydroxy-β-amyrin but this is not thought to be part of glycyrrhizin biosynthesis.
References:
1. Seki, H., Ohyama, K., Sawai, S., Mizutani, M., Ohnishi, T., Sudo, H., Akashi, T., Aoki, T., Saito, K. and Muranaka, T. Licorice β-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin. Proc. Natl. Acad. Sci. USA 105 (2008) 14204-14209. [PMID: 18779566]
EC 1.14.13.135
Accepted name: 1-hydroxy-2-naphthoate hydroxylase
Reaction: 1-hydroxy-2-naphthoate + NAD(P)H + H+ + O2 = 1,2-dihydroxynaphthalene + NAD(P)+ + H2O + CO2
Other name(s): 1-hydroxy-2-naphthoic acid hydroxylase
Systematic name: 1-hydroxy-2-naphthoate,NAD(P)H:oxygen oxidoreductase (2-hydroxylating, decarboxylating)
Comments: The enzyme is involved in the catabolic pathway for the degradation of chrysene in some bacteria [2].
References:
1. Deveryshetty, J. and Phale, P.S. Biodegradation of phenanthrene by Alcaligenes sp. strain PPH: partial purification and characterization of 1-hydroxy-2-naphthoic acid hydroxylase. FEMS Microbiol. Lett. 311 (2010) 93-101. [PMID: 20727010]
2. Nayak, A.S., Sanjeev Kumar, S., Santosh Kumar, M., Anjaneya, O. and Karegoudar, T.B. A catabolic pathway for the degradation of chrysene by Pseudoxanthomonas sp. PNK-04. FEMS Microbiol. Lett. 320 (2011) 128-134. [PMID: 21545490]
EC 1.14.13.136
Accepted name: isoflavonoid synthase
Reaction: liquiritigenin + O2 + NADPH + H+ = 2,7,4'-trihydroxyisoflavanone + H2O + NADP+
For diagram of reaction click here.
Glossary: liquiritigenin = 7,4'-dihydroxyflavanone
Other name(s): CYT93C; IFS; 2-hydroxyisoflavanone synthase (ambiguous)
Systematic name: liquiritigenin,NADPH:oxygen oxidoreductase (hydroxylating, aryl migration)
Comments: Requires cytochrome P450. The reaction involves the migration of the 2-phenyl group of the flavanone liquiritigenin to the 3-position of the isoflavanone. The 2-hydroxyl group is derived from the oxygen molecule.
References:
1. Hashim, M.F., Hakamatsuka, T., Ebizuka, Y. and Sankawa, U. Reaction mechanism of oxidative rearrangement of flavanone in isoflavone biosynthesis. FEBS Lett. 271 (1990) 219-222. [PMID: 2226805]
2. Sawada, Y., Kinoshita, K., Akashi, T., Aoki, T. and Ayabe, S. Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase. Plant J. 31 (2002) 555-564. [PMID: 12207646]
3. Sawada, Y. and Ayabe, S. Multiple mutagenesis of P450 isoflavonoid synthase reveals a key active-site residue. Biochem. Biophys. Res. Commun. 330 (2005) 907-913. [PMID: 15809082]
EC 1.14.14.11
Accepted name: styrene monooxygenase
Reaction: styrene + FADH2 + O2 = (S)-2-phenyloxirane + FAD + H2O
Other name(s): StyA; SMO; NSMOA
Systematic name: styrene,FADH2:oxygen oxidoreductase
Comments: The enzyme catalyses the first step in the aerobic styrene degradation pathway. It forms a two-component system with a reductase (StyB) that utilizes NADH to reduce flavin-adenine dinucleotide, which is then transferred to the oxygenase.
References:
1. Otto, K., Hofstetter, K., Rothlisberger, M., Witholt, B. and Schmid, A. Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120 as a two-component flavin-diffusible monooxygenase. J. Bacteriol. 186 (2004) 5292-5302. [PMID: 15292130]
2. Tischler, D., Kermer, R., Groning, J.A., Kaschabek, S.R., van Berkel, W.J. and Schlomann, M. StyA1 and StyA2B from Rhodococcus opacus 1CP: a multifunctional styrene monooxygenase system. J. Bacteriol. 192 (2010) 5220-5227. [PMID: 20675468]
EC 1.14.14.12
Accepted name: 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase
Reaction: 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMNH2 + O2 = 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMN + H2O
Other name(s): HsaA
Systematic name: 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione,FMNH2:oxygen oxidoreductase
Comments: This bacterial enzyme participates in the degradation of several steroids, including cholesterol and testosterone. It can use either FADH or FMNH2 as flavin cofactor. The enzyme forms a two-component system with a reductase (HsaB) that utilizes NADH to reduce the flavin, which is then transferred to the oxygenase subunit.
References:
1. Dresen, C., Lin, L.Y., D'Angelo, I., Tocheva, E.I., Strynadka, N. and Eltis, L.D. A flavin-dependent monooxygenase from Mycobacterium tuberculosis involved in cholesterol catabolism. J. Biol. Chem. 285 (2010) 22264-22275. [PMID: 20448045]
EC 1.16.9 With a copper protein as acceptor
EC 1.16.9.1
Accepted name: iron:rusticyanin reductase
Reaction: Fe(II) + rusticyanin = Fe(III) + reduced rusticyanin
Other name(s): Cyc2
Systematic name: Fe(II):rusticyanin oxidoreductase
Comments: Contains c-type heme, The enzyme in Acidithiobacillus ferrooxidans is a component of an electron transfer chain from Fe(II), comprising this enzyme, the copper protein rusticyanin, cytochrome c4, and cytochrome c oxidase (EC 1.9.3.1)
References:
1. Blake, R.C., 2nd and Shute, E.A. Respiratory enzymes of Thiobacillus ferrooxidans. Kinetic properties of an acid-stable iron:rusticyanin oxidoreductase. Biochemistry 33 (1994) 9220-9228. [PMID: 8049223]
2. Appia-Ayme, C., Bengrine, A., Cavazza, C., Giudici-Orticoni, M.T., Bruschi, M., Chippaux, M. and Bonnefoy, V. Characterization and expression of the co-transcribed cyc1 and cyc2 genes encoding the cytochrome c4 (c552) and a high-molecular-mass cytochrome c from Thiobacillus ferrooxidans ATCC 33020. FEMS Microbiol. Lett. 167 (1998) 171-177. [PMID: 9809418]
3. Yarzabal, A., Brasseur, G., Ratouchniak, J., Lund, K., Lemesle-Meunier, D., DeMoss, J.A. and Bonnefoy, V. The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. J. Bacteriol. 184 (2002) 313-317. [PMID: 11741873]
4. Yarzabal, A., Appia-Ayme, C., Ratouchniak, J. and Bonnefoy, V. Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150 (2004) 2113-2123. [PMID: 15256554]
5. Taha, T.M., Kanao, T., Takeuchi, F. and Sugio, T. Reconstitution of iron oxidase from sulfur-grown Acidithiobacillus ferrooxidans. Appl. Environ. Microbiol. 74 (2008) 6808-6810. [PMID: 18791023]
6. Castelle, C., Guiral, M., Malarte, G., Ledgham, F., Leroy, G., Brugna, M. and Giudici-Orticoni, M.T. A new iron-oxidizing/O2-reducing supercomplex spanning both inner and outer membranes, isolated from the extreme acidophile Acidithiobacillus ferrooxidans. J. Biol. Chem. 283 (2008) 25803-25811. [PMID: 18632666]
7. Quatrini, R., Appia-Ayme, C., Denis, Y., Jedlicki, E., Holmes, D.S. and Bonnefoy, V. Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10 (2009) 394. [PMID: 19703284]
[EC 1.16.98.1 Transferred entry: Now EC 1.16.9.1 iron:rusticyanin reductase (EC 1.16.98.1 created 2011, deleted 2011)]
EC 1.17.1.7
Accepted name: 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
Reaction: 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP+ + H2O = 3-oxo-5,6-dehydrosuberyl-CoA + NADPH + H+
Glossary: 3-oxo-5,6-dehydrosuberyl-CoA = 3,8-dioxooct-5-enoyl-CoA
Other name(s): paaZ (gene name)
Systematic name: 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde:NADP+ oxidoreductase
Comments: The enzyme from Escherichia coli is a bifunctional fusion protein that also catalyses EC 3.7.1.16, oxepin-CoA hydrolase. Combined the two activities result in a two-step conversion of oxepin-CoA to 3-oxo-5,6-dehydrosuberyl-CoA, part of an aerobic phenylacetate degradation pathway.
References:
1. Ferrandez, A., Minambres, B., Garcia, B., Olivera, E.R., Luengo, J.M., Garcia, J.L. and Diaz, E. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273 (1998) 25974-25986. [PMID: 9748275]
2. Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047-3054. [PMID: 12846838]
3. Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390-14395. [PMID: 20660314]
EC 1.17.7.2
Accepted name: 7-hydroxymethyl chlorophyll a reductase
Reaction: 71-hydroxychlorophyll a + 2 reduced ferredoxin + 2 H+ = chlorophyll a + 2 oxidized ferredoxin + H2O
For diagram of reaction click here
Glossary: 71-hydroxychlorophyll a = 7-hydroxymethyl-chlorophyll a
Other name(s): HCAR
Systematic name: 71-hydroxychlorophyll a:ferredoxin oxidoreductase
Comments: Contains FAD and an iron-sulfur center. This enzyme, which is present in plant chloroplasts, carries out the second step in the conversion of chlorophyll b to chlorophyll a (cf. EC 1.1.1.294, chlorophyll(ide) b reductase). It similarly reduces chlorophyllide a.
References:
1. Meguro, M., Ito, H., Takabayashi, A., Tanaka, R. and Tanaka, A. Identification of the 7-hydroxymethyl chlorophyll a reductase of the chlorophyll cycle in Arabidopsis. Plant Cell 23 (2011) 3442-3453. [PMID: 21934147]
*EC 2.1.1.42
Accepted name: flavone 3'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3'-hydroxyflavone = S-adenosyl-L-homocysteine + 3'-methoxyflavone
For diagram of reaction click here
Other name(s): o-dihydric phenol methyltransferase; luteolin methyltransferase; luteolin 3'-O-methyltransferase; o-diphenol m-O-methyltransferase; o-dihydric phenol meta-O-methyltransferase; S-adenosylmethionine:flavone/flavonol 3'-O-methyltransferase; quercetin 3'-O-methyltransferase
Systematic name: S-adenosyl-L-methionine:3'-hydroxyflavone 3'-O-methyltransferase
Comments: The enzyme prefers flavones with vicinal 3',4'-dihydroxyl groups.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37205-55-3
References:
1. Ebel, J., Hahlbrock, K. and Grisebach, H. Purification and properties of an o-dihydricphenol meta-O-methyltransferase from cell suspension cultures of parsley and its relation to flavonoid biosynthesis. Biochim. Biophys. Acta 268 (1972) 313-326. [PMID: 5026305]
2. Muzac, I., Wang, J., Anzellotti, D., Zhang, H. and Ibrahim, R.K. Functional expression of an Arabidopsis cDNA clone encoding a flavonol 3'-O-methyltransferase and characterization of the gene product. Arch. Biochem. Biophys. 375 (2000) 385-388. [PMID: 10700397]
3. Poulton, J.E., Hahlbrock, K. and Grisebach, H. O-Methylation of flavonoid substrates by a partially purified enzyme from soybean cell suspension cultures. Arch. Biochem. Biophys. 180 (1977) 543-549. [PMID: 18099]
4. Kim, B.G., Lee, H.J., Park, Y., Lim, Y. and Ahn, J.H. Characterization of an O-methyltransferase from soybean. Plant Physiol. Biochem. 44 (2006) 236-241. [PMID: 16777424]
5. Lee, Y.J., Kim, B.G., Chong, Y., Lim, Y. and Ahn, J.H. Cation dependent O-methyltransferases from rice. Planta 227 (2008) 641-647. [PMID: 17943312]
*EC 2.1.1.74
Accepted name: methylenetetrahydrofolate—tRNA-(uracil54-C5)-methyltransferase (FADH2-oxidizing)
Reaction: 5,10-methylenetetrahydrofolate + uridine54 in tRNA + FADH2 = tetrahydrofolate + 5-methyluridine54 in tRNA + FAD
Glossary: Ψ = pseudouridine
Other name(s): folate-dependent ribothymidyl synthase; methylenetetrahydrofolate-transfer ribonucleate uracil 5-methyltransferase; 5,10-methylenetetrahydrofolate:tRNA-UPsiC (uracil-5-)-methyl-transferase; 5,10-methylenetetrahydrofolate:tRNA (uracil-5-)-methyl-transferase; TrmFO; folate/FAD-dependent tRNA T54 methyltransferase
Systematic name: 5,10-methylenetetrahydrofolate:tRNA (uracil54-C5)-methyltransferase
Comments: Up to 25% of the bases in mature tRNA are post-translationally modified or hypermodified. One almost universal post-translational modification is the conversion of U54 into ribothymidine in the TPsiC loop, and this modification is found in most species studied to date [2]. Unlike this enzyme, which uses 5,10-methylenetetrahydrofolate and FADH2 to supply the atoms for methylation of U54, EC 2.1.1.35, tRNA (uracil54-C5)-methyltransferase, uses S-adenosyl-L-methionine.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 56831-74-4
References:
1. Delk, A.S., Nagle, D.P., Jr. and Rabinowitz, J.C. Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2. J. Biol. Chem. 255 (1980) 4387-4390. [PMID: 6768721]
2. Becker, H.F., Motorin, Y., Sissler, M., Florentz, C. and Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274 (1997) 505-518. [PMID: 9417931]
3. Nishimasu, H., Ishitani, R., Yamashita, K., Iwashita, C., Hirata, A., Hori, H. and Nureki, O. Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc. Natl. Acad. Sci. USA 106 (2009) 8180-8185. [PMID: 19416846]
EC 2.1.1.233
Accepted name: [phosphatase 2A protein]-leucine-carboxy methyltransferase
Reaction: S-adenosyl-L-methionine + [phosphatase 2A protein]-leucine = S-adenosyl-L-homocysteine + [phosphatase 2A protein]-leucine methyl ester
Other name(s): leucine carboxy methyltransferase-1; LCMT1
Systematic name: S-adenosyl-L-methionine:[phosphatase 2A protein]-leucine O-methyltransferase
Comments: Methylates the C-terminal leucine of phosphatase 2A. A key regulator of protein phosphatase 2A. The methyl ester is hydrolysed by EC 3.1.1.89 (protein phosphatase methylesterase-1). Occurs mainly in the cytoplasm, Golgi region and late endosomes.
References:
1. De Baere, I., Derua, R., Janssens, V., Van Hoof, C., Waelkens, E., Merlevede, W. and Goris, J. Purification of porcine brain protein phosphatase 2A leucine carboxyl methyltransferase and cloning of the human homologue. Biochemistry 38 (1999) 16539-16547. [PMID: 10600115]
2. Tsai, M.L., Cronin, N. and Djordjevic, S. The structure of human leucine carboxyl methyltransferase 1 that regulates protein phosphatase PP2A. Acta Crystallogr. D Biol. Crystallogr. 67 (2011) 14-24. [PMID: 21206058]
EC 2.1.1.234
Accepted name: dTDP-3-amino-3,4,6-trideoxy-α-D-glucopyranose N,N-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + dTDP-3-amino-3,4,6-trideoxy-α-D-glucopyranose = 2 S-adenosyl-L-homocysteine + dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose
Glossary: α-D-desosamine = 3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose
Other name(s): DesVI
Systematic name: S-adenosyl-L-methionine:dTDP-3-amino-3,4,6-trideoxy-α-D-glucopyranose 3-N,N-dimethyltransferase
Comments: The enzyme is involved in the biosynthesis of desosamine, a 3-(dimethylamino)-3,4,6-trideoxyhexose found in certain macrolide antibiotics such as erthyromycin, azithromycin, and clarithromycin.
References:
1. Chen, H., Yamase, H., Murakami, K., Chang, C.W., Zhao, L., Zhao, Z. and Liu, H.W. Expression, purification, and characterization of two N,N-dimethyltransferases, tylM1 and desVI, involved in the biosynthesis of mycaminose and desosamine. Biochemistry 41 (2002) 9165-9183. [PMID: 12119032]
2. Burgie, E.S. and Holden, H.M. Three-dimensional structure of DesVI from Streptomyces venezuelae: a sugar N,N-dimethyltransferase required for dTDP-desosamine biosynthesis. Biochemistry 47 (2008) 3982-3988. [PMID: 18327916]
EC 2.1.1.235
Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose N,N-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose = 2 S-adenosyl-L-homocysteine + dTDP-3-dimethylamino-3,6-dideoxy-α-D-glucopyranose
Glossary: dTDP-D-mycaminose = dTDP-3-dimethylamino-3,6-dideoxy-α-D-glucopyranose
Other name(s): TylM1
Systematic name: S-adenosyl-L-methionine:dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose 3-N,N-dimethyltransferase
Comments: The enzyme is involved in the biosynthesis of mycaminose, an essential structural component of the macrolide antibiotic tylosin, which is produced by the bacterium Streptomyces fradiae.
References:
1. Chen, H., Yamase, H., Murakami, K., Chang, C.W., Zhao, L., Zhao, Z. and Liu, H.W. Expression, purification, and characterization of two N,N-dimethyltransferases, tylM1 and desVI, involved in the biosynthesis of mycaminose and desosamine. Biochemistry 41 (2002) 9165-9183. [PMID: 12119032]
2. Carney, A.E. and Holden, H.M. Molecular architecture of TylM1 from Streptomyces fradiae: an N,N-dimethyltransferase involved in the production of dTDP-D-mycaminose. Biochemistry 50 (2011) 780-787. [PMID: 21142177]
EC 2.1.1.236
Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose N,N-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose = 2 S-adenosyl-L-homocysteine + dTDP-3-dimethylamino-3,6-dideoxy-α-D-galactopyranose
Glossary: dTDP-3-dimethylamino-3,6-dideoxy-α-D-galactopyranose = dTDP-D-ravidosamine
Other name(s): RavNMT
Systematic name: S-adenosyl-L-methionine:dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N,N-dimethyltransferase
Comments: The enzyme is involved in the synthesis of dTDP-D-ravidosamine, the amino sugar moiety of the antibiotic ravidomycin V, which is produced by the bacterium Streptomyces ravidus.
References:
1. Kharel, M.K., Lian, H. and Rohr, J. Characterization of the TDP-D-ravidosamine biosynthetic pathway: one-pot enzymatic synthesis of TDP-D-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate. Org. Biomol. Chem. 9 (2011) 1799-1808. [PMID: 21264378]
EC 2.1.1.237
Accepted name: mycinamicin III 3"-O-methyltransferase
Reaction: S-adenosyl-L-methionine + mycinamicin III = S-adenosyl-L-homocysteine + mycinamicin IV
For diagram of reaction click here.
Glossary: mycinamicin III = [(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-2-O-methyl-β-D-allopyranoside
Other name(s): MycF
Systematic name: S-adenosyl-L-methionine:mycinamicin III 3"-O-methyltransferase
Comments: The enzyme is involved in the biosynthesis of mycinamicin macrolide antibiotics.
References:
1. Li, S., Anzai, Y., Kinoshita, K., Kato, F. and Sherman, D.H. Functional analysis of MycE and MycF, two O-methyltransferases involved in the biosynthesis of mycinamicin macrolide antibiotics. Chembiochem. 10 (2009) 1297-1301. [PMID: 19415708]
EC 2.1.1.238
Accepted name: mycinamicin VI 2"-O-methyltransferase
Reaction: S-adenosyl-L-methionine + mycinamicin VI = S-adenosyl-L-homocysteine + mycinamicin III
For diagram of reaction click here.
Glossary: mycinamicin III = [(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-2-O-methyl-β-D-allopyranoside
Other name(s): MycE
Systematic name: S-adenosyl-L-methionine:mycinamicin VI 2"-O-methyltransferase
Comments: The enzyme is involved in the biosynthesis of mycinamicin macrolide antibiotics. Requires Mg2+ for optimal activity.
References:
1. Li, S., Anzai, Y., Kinoshita, K., Kato, F. and Sherman, D.H. Functional analysis of MycE and MycF, two O-methyltransferases involved in the biosynthesis of mycinamicin macrolide antibiotics. Chembiochem. 10 (2009) 1297-1301. [PMID: 19415708]
*EC 2.3.1.135
Accepted name: phosphatidylcholine—retinol O-acyltransferase
Reaction: phosphatidylcholine + retinol—[cellular-retinol-binding-protein] = 2-acylglycerophosphocholine + retinyl-ester—[cellular-retinol-binding-protein]
Glossary: phosphatidylcholine = lecithin
Other name(s): lecithin—retinol acyltransferase; phosphatidylcholine:retinol-(cellular-retinol-binding-protein) O-acyltransferase; lecithin:retinol acyltransferase; lecithin-retinol acyltransferase; retinyl ester synthase; LRAT; lecithin retinol acyl transferase
Systematic name: phosphatidylcholine:retinol—[cellular-retinol-binding-protein] O-acyltransferase
Comments: A key enzyme in retinoid metabolism, catalysing the transfer of an acyl group from the sn-1 position of phosphatidylcholine to retinol, forming retinyl esters which are then stored. Recognizes the substrate both in free form and when bound to cellular-retinol-binding-protein, but has higher affinity for the bound form. Can also esterify 11-cis-retinol.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 117444-03-8
References:
1. MacDonald, P.N. and Ong, D.E. Evidence for a lecithin-retinol acyltransferase activity in the rat small intestine. J. Biol. Chem. 263 (1988) 12478-12482. [PMID: 3410848]
2. Saari, J.C. and Bredberg, D.L. Lecithin:retinol acyltransferase in retinal pigment epithelial microsomes. J. Biol. Chem. 264 (1989) 8636. [PMID: 2722792]
3. Saari, J.C., Bredberg, D.L. and Farrell, D.F. Retinol esterification in bovine retinal pigment epithelium: reversibility of lecithin:retinol acyltransferase. Biochem. J. 291 (1993) 697-700. [PMID: 8489497]
4. Mata, N.L. and Tsin, A.T. Distribution of 11-cis LRAT, 11-cis RD and 11-cis REH in bovine retinal pigment epithelium membranes. Biochim. Biophys. Acta 1394 (1998) 16-22. [PMID: 9767084]
5. Ruiz, A., Winston, A., Lim, Y.H., Gilbert, B.A., Rando, R.R. and Bok, D. Molecular and biochemical characterization of lecithin retinol acyltransferase. J. Biol. Chem. 274 (1999) 3834-3841. [PMID: 9920938]
*EC 2.3.2.2
Accepted name: γ-glutamyltransferase
Reaction: a (5-L-glutamyl)-peptide + an amino acid = a peptide + a 5-L-glutamyl amino acid
Other name(s): glutamyl transpeptidase; α-glutamyl transpeptidase; γ-glutamyl peptidyltransferase; γ-glutamyl transpeptidase (ambiguous); γ-GPT; γ-GT; γ-GTP; L-γ-glutamyl transpeptidase; L-γ-glutamyltransferase; L-glutamyltransferase; GGT (ambiguous); γ-glutamyltranspeptidase (ambiguous)
Systematic name: (5-L-glutamyl)-peptide:amino-acid 5-glutamyltransferase
Comments: The mammlian enzyme is part of the cell antioxidant defense mechanism. It initiates extracellular glutathione (GSH) breakdown, provides cells with a local cysteine supply and contributes to maintain intracelular GSH levels. The protein also has EC 3.4.19.13 (glutathione hydrolase) activity [3-4]. The enzyme consists of two chains that are created by the proteolytic cleavage of a single precursor polypeptide. The N-terminal L-threonine of the C-terminal subunit functions as the active site for both the cleavage and the hydrolysis reactions [3-4].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number: 9046-27-9
References:
1. Goore, M.Y. and Thompson, J.F. γ-Glutamyl transpeptidase from kidney bean fruit. I. Purification and mechanism of action. Biochim. Biophys. Acta 132 (1967) 15-26. [PMID: 6030345]
2. Leibach, F.H. and Binkley, F. γ-Glutamyl transferase of swine kidney. Arch. Biochem. Biophys. 127 (1968) 292-301. [PMID: 5698023]
3. Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structures of γ-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc. Natl. Acad. Sci. USA 103 (2006) 6471-6476. [PMID: 16618936]
4. Boanca, G., Sand, A., Okada, T., Suzuki, H., Kumagai, H., Fukuyama, K. and Barycki, J.J. Autoprocessing of Helicobacter pylori γ-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad. J. Biol. Chem. 282 (2007) 534-541. [PMID: 17107958]
5. Wickham, S., West, M.B., Cook, P.F. and Hanigan, M.H. Gamma-glutamyl compounds: substrate specificity of γ-glutamyl transpeptidase enzymes. Anal. Biochem. 414 (2011) 208-214. [PMID: 21447318]
EC 2.4.1.277
Accepted name: glycosyltransferase DesVII
Reaction: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose + 10-deoxymethynolide = dTDP + 10-deoxymethymycin
For diagram of reaction click here.
Glossary: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose = dTDP-D-desosamine
Other name(s): DesVII
Systematic name: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:10-deoxymethynolide 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase
Comments: DesVII is the glycosyltransferase responsible for the attachment of TDP-D-desosamine to macrolactones of varied ring sizes. The enzyme is involved in the biosynthesis of methymycin, neomethymycin, narbomycin, and pikromycin in
Streptomyces venezuelae.
References:
1. Borisova, S.A. and Liu, H.W. Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry 49 (2010) 8071-8084. [PMID: 20695498]
2. Borisova, S.A., Kim, H.J., Pu, X. and Liu, H.W. Glycosylation of acyclic and cyclic aglycone substrates by macrolide glycosyltransferase DesVII/DesVIII: analysis and implications. Chembiochem. 9 (2008) 1554-1558. [PMID: 18548476]
3. Hong, J.S., Park, S.J., Parajuli, N., Park, S.R., Koh, H.S., Jung, W.S., Choi, C.Y. and Yoon, Y.J. Functional analysis of desVIII homologues involved in glycosylation of macrolide antibiotics by interspecies complementation. Gene 386 (2007) 123-130. [PMID: 17049185]
EC 2.5.1.97
Accepted name: pseudaminic acid synthase
Reaction: phosphoenolpyruvate + 2,4-bis(acetylamino)-2,4,6-trideoxy-β-L-altropyranose + H2O = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid + phosphate
Glossary: pseudaminic acid = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid
Other name(s): PseI; NeuB3
Systematic name: phosphoenolpyruvate:2,4-bis(acetylamino)-2,4,6-trideoxy-β-L-altropyranose transferase (phosphate-hydrolysing, 2,7-acetylamino-transfering, 2-carboxy-2-oxoethyl-forming)
Comments: The enzyme requires a divalent metal ion, the highest activity values are observed in the presence of Mn2+ and Co2+ (10 mM).
References:
1. Chou, W.K., Dick, S., Wakarchuk, W.W. and Tanner, M.E. Identification and characterization of NeuB3 from Campylobacter jejuni as a pseudaminic acid synthase. J. Biol. Chem. 280 (2005) 35922-35928. [PMID: 16120604]
EC 2.6.1.88
Accepted name: methionine transaminase
Reaction: L-methionine + a 2-oxo acid = 2-oxo-4-methylthiobutanoate + an L-amino acid
Other name(s): methionine-oxo-acid transaminase
Systematic name: L-methionine:2-oxo-acid aminotransferase
Comments: The enzyme is most active with L-methionine. It participates in the L-methionine salvage pathway from S-methyl-5'-thioadenosine, a by-product of polyamine biosynthesis. The enzyme from the bacterium Klebsiella pneumoniae can use several different amino acids as amino donor, with aromatic amino acids being the most effective [1]. The enzyme from the plant Arabidopsis thaliana is also a part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates [3].
References:
1. Heilbronn, J., Wilson, J. and Berger, B.J. Tyrosine aminotransferase catalyzes the final step of methionine recycling in Klebsiella pneumoniae. J. Bacteriol. 181 (1999) 1739-1747. [PMID: 10074065]
2. Dolzan, M., Johansson, K., Roig-Zamboni, V., Campanacci, V., Tegoni, M., Schneider, G. and Cambillau, C. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett. 571 (2004) 141-146. [PMID: 15280032]
3. Schuster, J., Knill, T., Reichelt, M., Gershenzon, J. and Binder, S. Branched-chain aminotransferase4 is part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates in Arabidopsis. Plant Cell 18 (2006) 2664-2679. [PMID: 17056707]
EC 2.6.1.89
Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose transaminase
Reaction: dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose + 2-oxoglutarate = dTDP-3-dehydro-6-deoxy-α-D-glucopyranose + L-glutamate
Glossary: dTDP-D-mycaminose = dTDP-3-dimethylamino-3,6-dideoxy-α-D-glucopyranose
Other name(s): TylB; TDP-3-keto-6-deoxy-D-glucose 3-aminotransferase; TDP-3-dehydro-6-deoxy-D-glucose 3-aminotransferase; dTDP-3-keto-6-deoxy-D-glucose 3-aminotransferase; dTDP-3-dehydro-6-deoxy-D-glucose 3-aminotransferase
Systematic name: dTDP-3-amino-3,6-dideoxy-α-D-glucopyranose:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. The reaction occurs in the reverse direction. The enzyme is involved in biosynthesis of D-mycaminose.
References:
1. Melancon, C.E., 3rd, Hong, L., White, J.A., Liu, Y.N. and Liu, H.W. Characterization of TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from the D-mycaminose biosynthetic pathway of Streptomyces fradiae: in vitro activity and substrate specificity studies. Biochemistry 46 (2007) 577-590. [PMID: 17209568]
EC 2.6.1.90
Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose transaminase
Reaction: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose + 2-oxoglutarate = dTDP-3-dehydro-6-deoxy-α-D-galactopyranose + L-glutamate
Glossary: dTDP-3-dehydro-6-deoxy-D-galactopyranose = dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
Other name(s): dTDP-6-deoxy-D-xylohex-3-uloseaminase; FdtB; TDP-3-keto-6-deoxy-D-galactose-3-aminotransferase; RavAMT; TDP-3-keto-6-deoxy-D-galactose 3-aminotransferase; TDP-3-dehydro-6-deoxy-D-galactose 3-aminotransferase
Systematic name: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. The enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose. The reaction occurs in the reverse direction.
References:
1. Pfoestl, A., Hofinger, A., Kosma, P. and Messner, P. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 278 (2003) 26410-26417. [PMID: 12740380]
EC 2.6.1.91
Accepted name: UDP-4-amino-4,6-dideoxy-α-D-N-acetyl-D-glucosamine transaminase
Reaction: UDP-4-amino-4,6-dideoxy-α-D-N-acetyl-D-glucosamine + 2-oxoglutarate = UDP-2-acetamido-2,6-dideoxy-α-D-xylo-4-hexulose + L-glutamate
Other name(s): PglE
Systematic name: UDP-4-amino-4,6-dideoxy-α-D-N-acetyl-D-glucosamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. The enzyme is involved in biosynthesis of bacillosamine.
References:
1. Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723-732. [PMID: 16286454]
EC 2.6.1.92
Accepted name: UDP-4-amino-4,6-dideoxy-L-N-acetyl-β-L-altrosamine transaminase
Reaction: UDP-4-amino-4,6-dideoxy-L-N-acetyl-β-L-altrosamine + 2-oxoglutarate = UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose + L-glutamate
Glossary: pseudaminic acid = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid
Other name(s): PseC
Systematic name: UDP-4-amino-4,6-dideoxy-L-N-acetyl-β-L-altrosamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. The enzyme is involved in biosynthesis of pseudaminic acid.
References:
1. Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723-732. [PMID: 16286454]
2. Schoenhofen, I.C., Lunin, V.V., Julien, J.P., Li, Y., Ajamian, E., Matte, A., Cygler, M., Brisson, J.R., Aubry, A., Logan, S.M., Bhatia, S., Wakarchuk, W.W. and Young, N.M. Structural and functional characterization of PseC, an aminotransferase involved in the biosynthesis of pseudaminic acid, an essential flagellar modification in Helicobacter pylori. J. Biol. Chem. 281 (2006) 8907-8916. [PMID: 16421095]
*EC 2.7.1.61
Accepted name: acyl-phosphate—hexose phosphotransferase
Reaction: acyl phosphate + D-hexose = a carboxylate + D-hexose phosphate
Other name(s): hexose phosphate:hexose phosphotransferase
Systematic name: acyl-phosphate:D-hexose phosphotransferase
Comments: Phosphorylates D-glucose and D-mannose on O-6, and D-fructose on O-1 or O-6.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37278-06-1
References:
1. Anderson, R.L. and Kamel, M.Y. Acyl phosphate:hexose phosphotransferase (hexose phosphate:hexose phosphotransferase). Methods Enzymol. 9 (1966) 392-396.
2. Kamel, M.Y. and Anderson, R.L. Acyl phosphate: hexose phosphotransferase. Purification and properties of the enzyme from Aerobacter aerogenes and evidence for its common identity with hexose phosphate: hexose phosphotransferase. Arch. Biochem. Biophys. 120 (1967) 322-331. [PMID: 6033450]
3. Casazza, J.P. and Fromm, H.J. Purification and initial rate kinetics of acyl-phosphate-hexose phosphotransferase from Aerobacter aerogenes. Biochemistry 16 (1977) 3091-3097. [PMID: 196625]
EC 2.7.7.80
Accepted name: molybdopterin-synthase adenylyltransferase
Reaction: ATP + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly = diphosphate + [molybdopterin-synthase sulfur-carrier protein]-Gly-Gly-AMP
For diagram of reaction click here.
Glossary: small subunit of the molybdopterin synthase = molybdopterin-synthase sulfur-carrier protein = MoaD
Other name(s): MoeB; adenylyltransferase and sulfurtransferase MOCS3
Systematic name: ATP:molybdopterin-synthase adenylyltransferase
Comments: Adenylates the C-terminus of the small subunit of the molybdopterin synthase. This activation is required to form the thiocarboxylated C-terminus of the active molybdopterin synthase small subunit. The reaction occurs in prokaryotes and eukaryotes. In the human, the reaction is catalysed by the N-terminal domain of the protein MOCS3, which also includes a molybdopterin-synthase sulfurtransferase (EC 2.8.1.11) C-terminal domain.
References:
1. Leimkuhler, S., Wuebbens, M.M. and Rajagopalan, K.V. Characterization of Escherichia coli MoeB and its involvement in the activation of molybdopterin synthase for the biosynthesis of the molybdenum cofactor. J. Biol. Chem. 276 (2001) 34695-34701. [PMID: 11463785]
2. 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]
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 = AMP + [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + cysteine desulfurase
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.
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 2.8.1.12
Accepted name: molybdopterin synthase
Reaction: cyclic pyranopterin monophosphate + 2 [molybdopterin-synthase sulfur-carrier protein]-Gly-NH-CH2-C(O)SH + H2O = molybdopterin + 2 molybdopterin-synthase sulfur-carrier protein
For diagram of reaction click here.
Glossary: molybdopterin =H2Dtpp-mP = {[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-κS)-1,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)molybdate(2-)
Other name(s): MPT synthase
Systematic name: thiocarboxylated molybdopterin synthase:cyclic pyranopterin monophosphate sulfurtransferase
Comments: Catalyses the synthesis of molybdopterin from cyclic pyranopterin monophosphate. Two sulfur atoms are transferred to cyclic pyranopterin monophosphate in order to form the characteristic ene-dithiol group found in the molybdenum cofactor. Molybdopterin synthase consists of two large subunits forming a central dimer and two small subunits (molybdopterin-synthase sulfur-carrier proteins) that are thiocarboxylated at the C-terminus by EC 2.8.1.11, molybdopterin synthase sulfurtransferase. The reaction occurs in prokaryotes and eukaryotes.
References:
1. Daniels, J.N., Wuebbens, M.M., Rajagopalan, K.V. and Schindelin, H. Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency. Biochemistry 47 (2008) 615-626. [PMID: 18092812]
2. Wuebbens, M.M. and Rajagopalan, K.V. Mechanistic and mutational studies of Escherichia coli molybdopterin synthase clarify the final step of molybdopterin biosynthesis. J. Biol. Chem. 278 (2003) 14523-14532. [PMID: 12571226]
*EC 3.1.1.64
Accepted name: retinoid isomerohydrolase
Reaction: an all-trans-retinyl ester + H2O = 11-cis-retinol + a fatty acid
For diagram of reaction click here.
Other name(s): all-trans-retinyl-palmitate hydrolase (ambiguous); retinol isomerase (ambiguous); all-trans-retinol isomerase:hydrolase (ambiguous); all-trans-retinylester 11-cis isomerohydrolase; RPE65 (gene name)
Systematic name: all-trans-retinyl ester acylhydrolase, 11-cis retinol forming
Comments: This enzyme, which operates in the retinal pigment epithelium (RPE), catalyses the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol, a key step in the regeneration of the visual chromophore in the vertebrate visual cycle [4]. Interaction of the enzyme with the membrane is critical for its enzymatic activity [6].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 106389-24-6
References:
1. Blaner, W.S., Das, S.R., Gouras, P. and Flood, M.T. Hydrolysis of 11-cis- and all-trans-retinyl palmitate by homogenates of human retinal epithelial cells. J. Biol. Chem. 262 (1987) 53-58. [PMID: 3793734]
2. Bernstein, P.S., Law, W.C. and Rando, R.R. Isomerization of all-trans-retinoids to 11-cis-retinoids in vitro. Proc. Natl. Acad. Sci. USA 84 (1987) 1849-1853. [PMID: 3494246]
3. Bridges, C.D. and Alvarez, R.A. The visual cycle operates via an isomerase acting on all-trans retinol in the pigment epithelium. Science 236 (1987) 1678-1680. [PMID: 3603006]
4. Moiseyev, G., Chen, Y., Takahashi, Y., Wu, B.X. and Ma, J.X. RPE65 is the isomerohydrolase in the retinoid visual cycle. Proc. Natl. Acad. Sci. USA 102 (2005) 12413-12418. [PMID: 16116091]
5. Nikolaeva, O., Takahashi, Y., Moiseyev, G. and Ma, J.X. Purified RPE65 shows isomerohydrolase activity after reassociation with a phospholipid membrane. FEBS J. 276 (2009) 3020-3030. [PMID: 19490105]
6. Golczak, M., Kiser, P.D., Lodowski, D.T., Maeda, A. and Palczewski, K. Importance of membrane structural integrity for RPE65 retinoid isomerization activity. J. Biol. Chem. 285 (2010) 9667-9682. [PMID: 20100834]
EC 3.1.1.89
Accepted name: protein phosphatase methylesterase-1
Reaction: [phosphatase 2A protein]-leucine methyl ester + H2O = [phosphatase 2A protein]-leucine + methanol
Other name(s): PME-1; PPME1
Systematic name: [phosphatase 2A protein]-leucine ester acylhydrolase
Comments: A key regulator of protein phosphatase 2A. The methyl ester is formed by EC 2.1.1.233 (leucine carboxy methyltransferase-1). Occurs mainly in the nucleus.
References:
1. Ogris, E., Du, X., Nelson, K.C., Mak, E.K., Yu, X.X., Lane, W.S. and Pallas, D.C. A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A. J. Biol. Chem. 274 (1999) 14382-14391. [PMID: 10318862]
2. Xing, Y., Li, Z., Chen, Y., Stock, J.B., Jeffrey, P.D. and Shi, Y. Structural mechanism of demethylation and inactivation of protein phosphatase 2A. Cell 133 (2008) 154-163. [PMID: 18394995]
EC 3.1.1.90
Accepted name: all-trans-retinyl ester 13-cis isomerohydrolase
Reaction: an all-trans-retinyl ester + H2O = 13-cis-retinol + a fatty acid
For diagram of reaction click here.
Systematic name: all-trans-retinyl ester acylhydrolase, 13-cis retinol forming
Comments: All-trans-retinyl esters, which are a storage form of vitamin A, are generated by the activity of EC 2.3.1.135, phosphatidylcholine—retinol O-acyltransferase (LRAT). They can be hydrolysed to 11-cis-retinol by EC 3.1.1.64, retinoid isomerohydrolase (RPE65), or to 13-cis-retinol by this enzyme.
References:
1. Takahashi, Y., Moiseyev, G., Chen, Y., Farjo, K., Nikolaeva, O. and Ma, J.X. An enzymatic mechanism for generating the precursor of endogenous 13-cis retinoic acid in the brain. FEBS J. 278 (2011) 973-987. [PMID: 21235714]
EC 3.1.3.86
Accepted name: phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase
Reaction: 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphate + phosphate
Glossary: phosphatidylinositol-3,4-bisphosphate = PtdIns(3,4)P2
Other name(s): SHIP1; SHIP2; SHIP; p150Ship
Systematic name: 1-phosphatidyl-1D-myo-inositol-3,4,5-trisphosphate 5-phosphohydrolase
Comments: This enzyme hydroylses phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) to produce PtdIns(3,4)P2, thereby negatively regulating the PI3K (phosphoinositide 3-kinase) pathways. The enzyme also shows activity toward (PtdIns(1,3,4,5)P4) [5]. The enzyme is involved in several signal transduction pathways in the immune system leading to an adverse range of effects.
References:
1. Lioubin, M.N., Algate, P.A., Tsai, S., Carlberg, K., Aebersold, A. and Rohrschneider, L.R. p150Ship, a signal transduction molecule with inositol polyphosphate-5-phosphatase activity. Genes Dev. 10 (1996) 1084-1095. [PMID: 8654924]
2. Damen, J.E., Liu, L., Rosten, P., Humphries, R.K., Jefferson, A.B., Majerus, P.W. and Krystal, G. The 145-kDa protein induced to associate with Shc by multiple cytokines is an inositol tetraphosphate and phosphatidylinositol 3,4,5-triphosphate 5-phosphatase. Proc. Natl. Acad. Sci. USA 93 (1996) 1689-1693. [PMID: 8643691]
3. Giuriato, S., Payrastre, B., Drayer, A.L., Plantavid, M., Woscholski, R., Parker, P., Erneux, C. and Chap, H. Tyrosine phosphorylation and relocation of SHIP are integrin-mediated in thrombin-stimulated human blood platelets. J. Biol. Chem. 272 (1997) 26857-26863. [PMID: 9341117]
4. Drayer, A.L., Pesesse, X., De Smedt, F., Woscholski, R., Parker, P. and Erneux, C. Cloning and expression of a human placenta inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase. Biochem. Biophys. Res. Commun. 225 (1996) 243-249. [PMID: 8769125]
5. Pesesse, X., Moreau, C., Drayer, A.L., Woscholski, R., Parker, P. and Erneux, C. The SH2 domain containing inositol 5-phosphatase SHIP2 displays phosphatidylinositol 3,4,5-trisphosphate and inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity. FEBS Lett. 437 (1998) 301-303. [PMID: 9824312]
EC 3.1.7.8
Accepted name: tuberculosinol synthase
Reaction: tuberculosinyl diphosphate + H2O = tuberculosinol + diphosphate
For diagram of reaction click here.
Other name(s): Rv3378c
Systematic name: tuberculosinyl diphosphate diphosphohydrolase (tuberculosinol forming)
Comments: Only found in species of Mycobacterium that cause tuberculosis. In addition, it also gives isotuberculosinol in 1:1 mixture, cf EC 3.1.7.9, isotuberculosinol synthase.
References:
1. Nakano, C., Ootsuka, T., Takayama, K., Mitsui, T., Sato, T. and Hoshino, T. Characterization of the Rv3378c gene product, a new diterpene synthase for producing tuberculosinol and (13R,S)-isotuberculosinol (nosyberkol), from the Mycobacterium tuberculosis H37Rv genome. Biosci. Biotechnol. Biochem. 75 (2011) 75-81. [PMID: 21228491]
2. Hoshino, T., Nakano, C., Ootsuka, T., Shinohara, Y. and Hara, T. Substrate specificity of Rv3378c, an enzyme from Mycobacterium tuberculosis, and the inhibitory activity of the bicyclic diterpenoids against macrophage phagocytosis. Org. Biomol. Chem. 9 (2011) 2156-2165. [PMID: 21290071]
EC 3.1.7.9
Accepted name: isotuberculosinol synthase
Reaction: tuberculosinyl diphosphate + H2O = (13S)-isotuberculosinol + diphosphate
For diagram of reaction click here.
Other name(s): Rv3378c
Systematic name: tuberculosinyl diphosphate diphosphohydrolase (isotuberculosinol forming)
Comments: Only found in species of Mycobacterium that cause tuberculosis. In addition, it also gives tuberculosinol in 1:1 mixture, cf EC 3.1.7.8, tuberculosinol synthase. The isotuberculosinol form was a 3:1 mixture of the 13S and 13R forms, respectively.
References:
1. Nakano, C., Ootsuka, T., Takayama, K., Mitsui, T., Sato, T. and Hoshino, T. Characterization of the Rv3378c gene product, a new diterpene synthase for producing tuberculosinol and (13R,S)-isotuberculosinol (nosyberkol), from the Mycobacterium tuberculosis H37Rv genome. Biosci. Biotechnol. Biochem. 75 (2011) 75-81. [PMID: 21228491]
2. Hoshino, T., Nakano, C., Ootsuka, T., Shinohara, Y. and Hara, T. Substrate specificity of Rv3378c, an enzyme from Mycobacterium tuberculosis, and the inhibitory activity of the bicyclic diterpenoids against macrophage phagocytosis. Org. Biomol. Chem. 9 (2011) 2156-2165. [PMID: 21290071]
*EC 3.2.1.47
Accepted name: galactosylgalactosylglucosylceramidase
Reaction: α-D-galactosyl-(1→4)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide + H2O = D-galactose + β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide
For diagram of reaction click here.
Other name(s): trihexosyl ceramide galactosidase; ceramide trihexosidase; ceramidetrihexoside α-galactosidase; trihexosylceramide α-galactosidase; ceramidetrihexosidase
Systematic name: α-D-galactosyl-(1→4)-β-D-galactosyl-(1→4)-β-D-glucosyl-(1↔1)-ceramide galactohydrolase
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9023-01-2
References:
1. Brady, R.O., Gal, A.E., Bradley, R.M. and Matensson, E. The metabolism of ceramide trihexosides. I. Purification and properties of an enzyme that cleaves the terminal galactose molecule of galactosylgalactosylglucosylceramide. J. Biol. Chem. 242 (1967) 1021-1026. [PMID: 6020428]
2. Mapes, C.A. and Sweeley, C.C. Substrate specificity of ceramide trihexosidase. FEBS Lett. 25 (1972) 279-281. [PMID: 11946769]
EC 3.2.1.179
Accepted name: gellan tetrasaccharide unsaturated glucuronyl hydrolase
Reaction: β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-β-D-Glcp + H2O =
4-deoxy-L-threo-5-hexosulose-uronate + β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-β-D-Glcp
Other name(s): UGL (ambiguous); unsaturated glucuronyl hydrolase (ambiguous)
Systematic name: β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-β-D-Glcp β-D-4-deoxy-Δ4-GlcAp hydrolase
Comments: The enzyme releases 4-deoxy-4(5)-unsaturated D-glucuronic acid from oligosaccharides produced by polysaccharide lyases, e.g. the tetrasaccharide β-D-4-deoxy-Δ4-GlcAp-(1→4)-β-D-Glcp-(1→4)-α-L-Rhap-(1→3)-β-D-Glcp produced by EC 4.2.2.25, gellan lyase. The enzyme can also hydrolyse unsaturated chondroitin and hyaluronate disaccharides (β-D-4-deoxy-Δ4-GlcAp-(1→3)-β-D-GalNAc, β-D-4-deoxy-Δ4-GlcAp-(1→3)-β-D-GalNAc6S, β-D-4-deoxy-Δ4-GlcAp2S-(1→3)-β-D-GalNAc, β-D-4-deoxy-Δ4-GlcAp-(1→3)-β-D-GlcNAc), preferring the unsulfated disaccharides to the sulfated disaccharides.
References:
1. Itoh, T., Akao, S., Hashimoto, W., Mikami, B. and Murata, K. Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 Å resolution. J. Biol. Chem. 279 (2004) 31804-31812. [PMID: 15148314]
2. Hashimoto, W., Kobayashi, E., Nankai, H., Sato, N., Miya, T., Kawai, S. and Murata, K. Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases. Arch. Biochem. Biophys. 368 (1999) 367-374. [PMID: 10441389]
3. Itoh, T., Hashimoto, W., Mikami, B. and Murata, K. Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1. Biochem. Biophys. Res. Commun. 344 (2006) 253-262. [PMID: 16630576]
EC 3.2.1.180
Accepted name: unsaturated chondroitin disaccharide hydrolase
Reaction: β-D-4-deoxy-Δ4-GlcAp-(1→3)-β-D-GalNAc6S + H2O = 4-deoxy-L-threo-5-hexosulose-uronate + β-D-N-acetylgalactosamine-6-O-sulfate
Other name(s): UGL (ambiguous); unsaturated glucuronyl hydrolase (ambiguous)
Systematic name: β-D-4-deoxy-Δ4-GlcAp-(1→3)-β-D-GalNAc6S hydrolase
Comments: The enzyme releases 4-deoxy-4,5-didehydro D-glucuronic acid or 4-deoxy-4,5-didehydro L-iduronic acid from chondroitin disaccharides, hyaluronan disaccharides and heparin disaccharides and cleaves both glycosidic (1→3) and (1→4) bonds. It prefers the sulfated disaccharides to the unsulfated disaccharides.
References:
1. Maruyama, Y., Nakamichi, Y., Itoh, T., Mikami, B., Hashimoto, W. and Murata, K. Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. J. Biol. Chem. 284 (2009) 18059-18069. [PMID: 19416976]
2. Nakamichi, Y., Maruyama, Y., Mikami, B., Hashimoto, W. and Murata, K. Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups. J. Biol. Chem. 286 (2011) 6262-6271. [PMID: 21147778]
EC 3.4.19.13
Accepted name: glutathione hydrolase
Reaction: glutathione + H2O = L-cysteinylglycine + L-glutamate
Other name(s): glutathionase; GGT (ambiguous); γ-glutamyltranspeptidase (ambiguous)
Comments: This protein also has EC 2.3.2.2 (γ-glutamyltransferase) activity. The enzyme consists of two chains that are created by the proteolytic cleavage of a single precursor polypeptide. The N-terminal L-threonine of the C-terminal subunit functions as the active site for both the cleavage and the hydrolysis reactions [2-5]. The human enzyme also hydrolyses oxidized glutathione and leukotriene C4 with similar efficiency, while the mouse enzyme does not [6-7].
References:
1. Hanigan, M.H. and Ricketts, W.A. Extracellular glutathione is a source of cysteine for cells that express γ-glutamyl transpeptidase. Biochemistry 32 (1993) 6302-6306. [PMID: 8099811]
2. Suzuki, H. and Kumagai, H. Autocatalytic processing of γ-glutamyltranspeptidase. J. Biol. Chem. 277 (2002) 43536-43543. [PMID: 12207027]
3. Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structures of γ-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc. Natl. Acad. Sci. USA 103 (2006) 6471-6476. [PMID: 16618936]
4. Boanca, G., Sand, A., Okada, T., Suzuki, H., Kumagai, H., Fukuyama, K. and Barycki, J.J. Autoprocessing of Helicobacter pylori γ-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad. J. Biol. Chem. 282 (2007) 534-541. [PMID: 17107958]
5. Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structure of the γ-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism. J. Biol. Chem. 282 (2007) 2433-2439. [PMID: 17135273]
6. Wickham, S., West, M.B., Cook, P.F. and Hanigan, M.H. Gamma-glutamyl compounds: substrate specificity of γ-glutamyl transpeptidase enzymes. Anal. Biochem. 414 (2011) 208-214. [PMID: 21447318]
7. Carter, B.Z., Wiseman, A.L., Orkiszewski, R., Ballard, K.D., Ou, C.N. and Lieberman, M.W. Metabolism of leukotriene C4 in γ-glutamyl transpeptidase-deficient mice. J. Biol. Chem. 272 (1997) 12305-12310. [PMID: 9139674]
*EC 3.4.22.68
Accepted name: Ulp1 peptidase
Reaction: Hydrolysis of the α-linked peptide bond in the sequence Gly-Gly┼Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptide, Smt3, leading to the mature form of the protein. A second reaction involves the cleavage of an ε-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine ε-amino group of the target protein
Other name(s): Smt3-protein conjugate proteinase; Ubl-specific protease 1; Ulp1; Ulp1 endopeptidase; Ulp1 protease
Comments: The enzyme from Saccharomyces cerevisiae can also recognize small ubiquitin-like modifier 1 (SUMO-1) from human as a substrate in both SUMO-processing (α-linked peptide bonds) and SUMO-deconjugation (ε-linked peptide bonds) reactions [1,2,3]. Ulp1 has several functions, including an essential role in chromosomal segregation and progression of the cell cycle through the G2/M phase of the cell cycle. Belongs in peptidase family C48.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
CAS registry number:
References:
1. Lima, C.D. Ulp1 endopeptidase. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Eds), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 1340-1344.
2. Li, S.-J. and Hochstrasser, M. A new protease required for cell-cycle progression in yeast. Nature 398 (1999) 246-251. [PMID: 10094048]
3. Taylor, D.L., Ho, J.C., Oliver, A. and Watts, F.Z. Cell-cycle-dependent localisation of Ulp1, a Schizosaccharomyces pombe Pmt3 (SUMO)-specific protease. J. Cell Sci. 115 (2002) 1113-1122. [PMID: 11884512]
4. Li, S.-J. and Hochstrasser, M. The Ulp1 SUMO isopeptidase: distinct domains required for viability, nuclear envelope localization, and substrate specificity. J. Cell Biol. 160 (2003) 1069-1081. [PMID: 12654900]
5. Ihara, M., Koyama, H., Uchimura, Y., Saitoh, H. and Kikuchi, A. Noncovalent binding of small ubiquitin-related modifier (SUMO) protease to SUMO is necessary for enzymatic activities and cell growth. J. Biol. Chem. 282 (2007) 16465-16475. [PMID: 17428805]
6. Mukhopadhyay, D. and Dasso, M. Modification in reverse: the SUMO proteases. Trends Biochem. Sci. 32 (2007) 286-295. [PMID: 17499995]
EC 3.4.23.52
Accepted name: preflagellin peptidase
Reaction: Cleaves the signal peptide of 3 to 12 amino acids from the N-terminal of preflagellin, usually at Arg-Gly
Other name(s): FlaK
Comments: An aspartic peptidase from Archaea but not bacteria. In peptidase family A24 (type IV prepilin peptidase family).
References:
1. Bardy, S.L. and Jarrell, K.F. FlaK of the archaeon Methanococcus maripaludis possesses preflagellin peptidase activity. FEMS Microbiol. Lett. 208 (2002) 53-59. [PMID: 11934494]
2. Ng, S.Y., VanDyke, D.J., Chaban, B., Wu, J., Nosaka, Y., Aizawa, S. and Jarrell, K.F. Different minimal signal peptide lengths recognized by the archaeal prepilin-like peptidases FlaK and PibD. J. Bacteriol. 191 (2009) 6732-6740. [PMID: 19717585]
3. Hu, J., Xue, Y., Lee, S. and Ha, Y. The crystal structure of GXGD membrane protease FlaK. Nature 475 (2011) 528-531. [PMID: 21765428]
EC 3.5.1.109
Accepted name: sphingomyelin deacylase
Reaction: (1) an N-acyl-sphingosylphosphorylcholine + H2O = a fatty acid + sphingosylphosphorylcholine
Glossary: sphingomyelin = N-acyl-sphingosylphosphorylcholine
Other name(s): SM deacylase; GcSM deacylase; glucosylceramide sphingomyelin deacylase; sphingomyelin glucosylceramide deacylase; SM glucosylceramide GCer deacylase; SM-GCer deacylase; SMGCer deacylase
Systematic name: N-acyl-sphingosylphosphorylcholine amidohydrolase
Comments: The enzyme is involved in the sphingolipid metabolism in the epidermis.
References:
1. Hara, J., Higuchi, K., Okamoto, R., Kawashima, M. and Imokawa, G. High-expression of sphingomyelin deacylase is an important determinant of ceramide deficiency leading to barrier disruption in atopic dermatitis. J. Invest. Dermatol. 115 (2000) 406-413. [PMID: 10951276]
2. Higuchi, K., Hara, J., Okamoto, R., Kawashima, M. and Imokawa, G. The skin of atopic dermatitis patients contains a novel enzyme, glucosylceramide sphingomyelin deacylase, which cleaves the N-acyl linkage of sphingomyelin and glucosylceramide. Biochem. J. 350 (2000) 747-756. [PMID: 10970788]
3. Ishibashi, M., Arikawa, J., Okamoto, R., Kawashima, M., Takagi, Y., Ohguchi, K. and Imokawa, G. Abnormal expression of the novel epidermal enzyme, glucosylceramide deacylase, and the accumulation of its enzymatic reaction product, glucosylsphingosine, in the skin of patients with atopic dermatitis. Lab. Invest. 83 (2003) 397-408. [PMID: 12649340]
*EC 3.5.99.2
Accepted name: aminopyrimidine aminohydrolase
Reaction: (1) 4-amino-5-aminomethyl-2-methylpyrimidine + H2O = 4-amino-5-hydroxymethyl-2-methylpyrimidine + ammonia
Other name(s): thiaminase, thiaminase II, tenA (gene name)
Systematic name: 4-amino-5-aminomethyl-2-methylpyrimidine aminohydrolase
Comments: Previously known as thiaminase II, this enzyme is involved in the regeneration of the thiamine pyrimidine from degraded products, rather than in thiamine degradation, and participates in thiamine salvage pathways.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
PDB,
UM-BBD,
CAS registry number: 9024-80-0
References:
1. Fujita, A., Nose, Y. and Kuratani, K. Second type of bacterial thiaminase. J. Vitaminol. (Kyoto) 1 (1954) 1-7. [PMID: 13243520]
2. Ikehata, H. Purification of thiaminase II. J. Gen. Appl. Microbiol. 6 (1960) 30-39.
3. Toms, A.V., Haas, A.L., Park, J.H., Begley, T.P. and Ealick, S.E. Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II. Biochemistry 44 (2005) 2319-2329. [PMID: 15709744]
4. Benach, J., Edstrom, W.C., Lee, I., Das, K., Cooper, B., Xiao, R., Liu, J., Rost, B., Acton, T.B., Montelione, G.T. and Hunt, J.F. The 2.35 Å structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 589-598. [PMID: 15858269]
5. Jenkins, A.H., Schyns, G., Potot, S., Sun, G. and Begley, T.P. A new thiamin salvage pathway. Nat. Chem. Biol. 3 (2007) 492-497. [PMID: 17618314]
6. Jenkins, A.L., Zhang, Y., Ealick, S.E. and Begley, T.P. Mutagenesis studies on TenA: a thiamin salvage enzyme from Bacillus subtilis. Bioorg. Chem. 36 (2008) 29-32. [PMID: 18054064]
7. French, J.B., Begley, T.P. and Ealick, S.E. Structure of trifunctional THI20 from yeast. Acta Crystallogr. D Biol. Crystallogr. 67 (2011) 784-791. [PMID: 21904031]
EC 3.6.1.55
Accepted name: 8-oxo-dGTP diphosphatase
Reaction: 8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate
Glossary: 8-oxo-dGTP = 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate
Other name(s): MutT; 7,8-dihydro-8-oxoguanine triphosphatase; 8-oxo-dGTPase; 7,8-dihydro-8-oxo-dGTP pyrophosphohydrolase
Systematic name: 8-oxo-dGTP diphosphohydrolase
Comments: This enzyme hydrolyses the phosphoanhydride bond between the α and β phosphate of 8-oxoguanine-containing nucleoside di- and triphosphates thereby preventing misincorporation of the oxidized purine nucleoside triphosphates into DNA . It does not hydrolyse 2-hydroxy-dATP (cf. EC 3.6.1.56, 2-hydroxy-dATP diphosphatase) [4]. Requires Mg2+.
References:
1. Ito, R., Hayakawa, H., Sekiguchi, M. and Ishibashi, T. Multiple enzyme activities of Escherichia coli MutT protein for sanitization of DNA and RNA precursor pools. Biochemistry 44 (2005) 6670-6674. [PMID: 15850400]
2. Yoshimura, K., Ogawa, T., Ueda, Y. and Shigeoka, S. AtNUDX1, an 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase, is responsible for eliminating oxidized nucleotides in Arabidopsis. Plant Cell Physiol. 48 (2007) 1438-1449. [PMID: 17804481]
3. Nakamura, T., Meshitsuka, S., Kitagawa, S., Abe, N., Yamada, J., Ishino, T., Nakano, H., Tsuzuki, T., Doi, T., Kobayashi, Y., Fujii, S., Sekiguchi, M. and Yamagata, Y. Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base. J. Biol. Chem. 285 (2010) 444-452. [PMID: 19864691]
4. Yonekura, S., Sanada, U. and Zhang-Akiyama, Q.M. CiMutT, an asidian MutT homologue, has a 7, 8-dihydro-8-oxo-dGTP pyrophosphohydrolase activity responsible for sanitization of oxidized nucleotides in Ciona intestinalis. Genes Genet Syst 85 (2010) 287-295. [PMID: 21178309]
EC 3.6.1.56
Accepted name: 2-hydroxy-dATP diphosphatase
Reaction: 2-hydroxy-dATP + H2O = 2-hydroxy-dAMP + diphosphate
Other name(s): NUDT1; MTH1; MTH2; oxidized purine nucleoside triphosphatase; (2'-deoxy) ribonucleoside 5'-triphosphate pyrophosphohydrolase
Systematic name: 2-hydroxy-dATP diphosphohydrolase
Comments: The enzyme hydrolyses oxidized purine nucleoside triphosphates such as 2-hydroxy-dATP, thereby preventing their misincorporation into DNA. It can also recognize 8-oxo-dGTP and 8-oxo-dATP, but with lower efficiency (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [3].
References:
1. Sakumi, K., Furuichi, M., Tsuzuki, T., Kakuma, T., Kawabata, S., Maki, H. and Sekiguchi, M. Cloning and expression of cDNA for a human enzyme that hydrolyzes 8-oxo-dGTP, a mutagenic substrate for DNA synthesis. J. Biol. Chem. 268 (1993) 23524-23530. [PMID: 8226881]
2. Kakuma, T., Nishida, J., Tsuzuki, T. and Sekiguchi, M. Mouse MTH1 protein with 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphatase activity that prevents transversion mutation. cDNA cloning and tissue distribution. J. Biol. Chem. 270 (1995) 25942-25948. [PMID: 7592783]
3. Fujikawa, K., Kamiya, H., Yakushiji, H., Fujii, Y., Nakabeppu, Y. and Kasai, H. The oxidized forms of dATP are substrates for the human MutT homologue, the hMTH1 protein. J. Biol. Chem. 274 (1999) 18201-18205. [PMID: 10373420]
4. Sakai, Y., Furuichi, M., Takahashi, M., Mishima, M., Iwai, S., Shirakawa, M. and Nakabeppu, Y. A molecular basis for the selective recognition of 2-hydroxy-dATP and 8-oxo-dGTP by human MTH1. J. Biol. Chem. 277 (2002) 8579-8587. [PMID: 11756418]
5. Fujikawa, K., Kamiya, H., Yakushiji, H., Nakabeppu, Y. and Kasai, H. Human MTH1 protein hydrolyzes the oxidized ribonucleotide, 2-hydroxy-ATP. Nucleic Acids Res. 29 (2001) 449-454. [PMID: 11139615]
EC 3.6.1.57
Accepted name: UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose hydrolase
Reaction: UDP-2,4-bis(acetamido)-2,4,6-trideoxy-β-L-altropyranose + H2O = 2,4-bis(acetamido)-2,4,6-trideoxy-β-L-altropyranose + UDP
Other name(s): PseG; UDP-6-deoxy-AltdiNAc hydrolase; Cj1312
Systematic name: UDP-2,4-bis(acetamido)-2,4,6-trideoxy-β-L-altropyranose hydrolase
Comments: The enzyme is involved in biosynthesis of pseudaminic acid.
References:
1. Liu, F. and Tanner, M.E. PseG of pseudaminic acid biosynthesis: a UDP-sugar hydrolase as a masked glycosyltransferase. J. Biol. Chem. 281 (2006) 20902-20909. [PMID: 16728396]
2. Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C. [PMID: 16751642]
EC 3.7.1.15
Accepted name: (+)-caryolan-1-ol synthase
Reaction: (+)-β-caryophyllene + H2O = (+)-caryolan-1-ol
For diagram of reaction click here.
Other name(s): GcoA
Systematic name: (+)-β-caryophyllene hydrolase [cyclizing, (+)-caryolan-1-ol-forming]
Comments: A multifunctional enzyme which also forms (+)-β-caryophyllene from farnesyl diphosphate [EC 4.2.3.89, (+)-β-caryophyllene synthase]. Three atoms of deuterium are incorporated into (+)-caryolan-1-ol in the presence of D2O. This is consistent with the proposed mechanism of formation.
References:
1. Nakano, C., Horinouchi, S. and Ohnishi, Y. Characterization of a novel sesquiterpene cyclase involved in (+)-caryolan-1-ol biosynthesis in Streptomyces griseus. J. Biol. Chem. 286 (2011) 27980-27987. [PMID: 21693706]
EC 3.7.1.16
Accepted name: oxepin-CoA hydrolase
Reaction: 2-oxepin-2(3H)-ylideneacetyl-CoA + H2O = 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde
Glossary: oxepin-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
Other name(s): paaZ (gene name)
Systematic name: 2-oxepin-2(3H)-ylideneacetyl-CoA hydrolyase
Comments: The enzyme from Escherichia coli is a bifunctional fusion protein that also catalyses EC 1.17.1.7, 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase. Combined the two activities result in a two-step conversion of oxepin-CoA to 3-oxo-5,6-dehydrosuberyl-CoA, part of an aerobic phenylacetate degradation pathway [1,3,4]. The enzyme from Escherichia coli also exhibits enoyl-CoA hydratase activity utilizing crotonyl-CoA as a substrate [2].
References:
1. Ferrandez, A., Minambres, B., Garcia, B., Olivera, E.R., Luengo, J.M., Garcia, J.L. and Diaz, E. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273 (1998) 25974-25986. [PMID: 9748275]
2. Park, S.J. and Lee, S.Y. Identification and characterization of a new enoyl coenzyme A hydratase involved in biosynthesis of medium-chain-length polyhydroxyalkanoates in recombinant Escherichia coli. J. Bacteriol. 185 (2003) 5391-5397. [PMID: 12949091]
3. Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047-3054. [PMID: 12846838]
4. Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390-14395. [PMID: 20660314]
*EC 4.2.1.83
Accepted name: 4-oxalmesaconate hydratase
Reaction: 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate + H2O
For diagram of reaction click here.
Other name(s): 4-carboxy-2-oxohexenedioate hydratase; 4-carboxy-2-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; oxalmesaconate hydratase; γ-oxalmesaconate hydratase; 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate 2,3-hydro-lyase; LigJ; GalB
Systematic name: (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate 1,2-hydro-lyase (2-hydroxy-4-oxobutane-1,2,4-tricarboxylate-forming)
Comments: This enzyme participates in the degradation of protocatechuate (via the meta-cleavage pathway), syringate and gallate, catalysing the reaction in the opposite direction [1-3]. It accepts the enol-form of 4-oxalomesaconate, 2-hydroxy-4-carboxy-hexa-2,4-dienedioate [4].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 85204-95-1
References:
1. Maruyama, K. Enzymes responsible for degradation of 4-oxalmesaconic acid in Pseudomonas ochraceae. J. Biochem. 93 (1983) 567-574. [PMID: 6841354]
2. Maruyama, K. Purification and properties of γ-oxalomesaconate hydratase from Pseudomonas ochraceae grown with phthalate. Biochem. Biophys. Res. Commun. 128 (1985) 271-277. [PMID: 3985968]
3. Hara, H., Masai, E., Katayama, Y. and Fukuda, M. The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 182 (2000) 6950-6957. [PMID: 11092855]
4. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]
*EC 4.2.3.57
Accepted name: (–)-β-caryophyllene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (–)-β-caryophyllene + diphosphate
For diagram of reaction click here.
Other name(s): β-caryophyllene synthase; (2E,6E)-farnesyl-diphosphate diphosphate-lyase (caryophyllene-forming)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(–)-caryophyllene-forming]
Comments: Widely distributed in higher plants, cf. EC 4.2.3.89 (+)-β-caryophyllene synthase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 110639-18-4
References:
1. Cai, Y., Jia, J.W., Crock, J., Lin, Z.X., Chen, X.Y. and Croteau, R. A cDNA clone for β-caryophyllene synthase from Artemisia annua. Phytochemistry 61 (2002) 523-529. [PMID: 12409018]
*EC 4.2.3.62
Accepted name: (–)-γ-cadinene synthase [(2Z,6E)-farnesyl diphosphate cyclizing]
Reaction: (2Z,6E)-farnesyl diphosphate = (–)-γ-cadinene + diphosphate
For diagram of reaction click here.
Other name(s): (–)-γ-cadinene cyclase
Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase [(–)-γ-cadinene-forming]
Comments: Isolated from the liverwort Heteroscyphus planus. cf EC 4.2.3.92 (+)-γ-cadinene synthase.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
References:
1. Nabeta, K., Fujita, M., Komuro, K., Katayama, K., and Takasawa, T. In vitro biosynthesis of cadinanes by cell-free extracts of cultured cells of Heteroscyphus planus. J. Chem. Soc., Perkin Trans. 1 (1997) 2065-2070.
EC 4.2.3.86
Accepted name: 7-epi-α-selinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = 7-epi-α-selinene + diphosphate
For diagram of reaction click here.
Glossary: 7-epi-α-selinene = (2S,4aR,8aR)-4a,8-dimethyl-2-(prop-1-en-2-yl)-1,2,3,4,4a,5,6,8a-octahydronaphthalene
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (7-epi-α-selinene-forming)
Comments: The recombinant enzyme from Vitis vinifera forms 49.5% (+)-valencene (cf. EC 4.2.3.73, valencene synthase) and 35.5% (–)-7-epi-α-selinene. Initial cyclization gives (+)-germacrene A in an enzyme bound form which is not released to the medium.
References:
1. Lucker, J., Bowen, P. and Bohlmann, J. Vitis vinifera terpenoid cyclases: functional identification of two sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (–)-germacrene D synthase and expression of mono- and sesquiterpene synthases in grapevine flowers and berries. Phytochemistry 65 (2004) 2649-2659. [PMID: 15464152]
2. Martin, D.M., Toub, O., Chiang, A., Lo, B.C., Ohse, S., Lund, S.T. and Bohlmann, J. The bouquet of grapevine (Vitis vinifera L. cv. Cabernet Sauvignon) flowers arises from the biosynthesis of sesquiterpene volatiles in pollen grains. Proc. Natl. Acad. Sci. USA 106 (2009) 7245-7250. [PMID: 19359488]
EC 4.2.3.87
Accepted name: α-guaiene synthase
Reaction: (2E,6E)-farnesyl diphosphate = α-guaiene + diphosphate
For diagram of reaction click here.
Other name(s): PatTps177 (gene name)
Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, α-guaiene-forming)
Comments: Requires Mg2+. The enzyme from Pogostemon cablin gives 13% α-guaiene as well as 37% (-)-patchoulol (see EC 4.2.3.70), 13% δ-guaiene (see EC 4.2.3.93), and traces of at least ten other sesquiterpenoids [1]. In Aquilaria crassna three clones of the enzyme gave about 80% δ-guaiene and 20% α-guaiene, with traces of α-humulene. A fourth clone gave 54% δ-guaiene and 45% α-guaiene [2].
References:
1. Deguerry, F., Pastore, L., Wu, S., Clark, A., Chappell, J. and Schalk, M. The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Arch. Biochem. Biophys. 454 (2006) 123-136. [PMID: 16970904]
2. Kumeta, Y. and Ito, M. Characterization of δ-guaiene synthases from cultured cells of Aquilaria, responsible for the formation of the sesquiterpenes in agarwood. Plant Physiol. 154 (2010) 1998-2007. [PMID: 20959422]
EC 4.2.3.88
Accepted name: viridiflorene synthase
Reaction: (2E,6E)-farnesyl diphosphate = viridiflorene + diphosphate
For diagram of reaction click here.
Other name(s): TPS31
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (viridiflorene-forming)
Comments: Viridiflorene is the only product of this enzyme from Solanum lycopersicum.
References:
1. Bleeker, P.M., Spyropoulou, E.A., Diergaarde, P.J., Volpin, H., De Both, M.T., Zerbe, P., Bohlmann, J., Falara, V., Matsuba, Y., Pichersky, E., Haring, M.A. and Schuurink, R.C. RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes. Plant Mol. Biol. 77 (2011) 323-326. [PMID: 21818683]
EC 4.2.3.89
Accepted name: (+)-β-caryophyllene synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (+)-β-caryophyllene + diphosphate
For diagram of reaction click here.
Other name(s): GcoA
Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-β-caryophyllene-forming]
Comments: A multifunctional enzyme which also converts the (+)-β-caryophyllene to (+)-caryolan-1-ol (see EC 3.7.1.15, (+)-caryolan-1-ol synthase). cf. EC 4.2.3.57 (–)-β-caryophyllene synthase.
References:
1. Nakano, C., Horinouchi, S. and Ohnishi, Y. Characterization of a novel sesquiterpene cyclase involved in (+)-caryolan-1-ol biosynthesis in Streptomyces griseus. J. Biol. Chem. 286 (2011) 27980-27987. [PMID: 21693706]
EC 4.2.3.90
Accepted name: 5-epi-α-selinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = 5-epi-α-selinene + diphosphate
For diagram of reaction click here.
Glossary: 5-epi-α-selinene = 5β-eudesma-3,11-diene = (2R,4aR,8aS)-1,2,3,4,4a,5,6,8a-octahydro-4a,8-dimethyl-2-(prop-1-en-2-yl)naphthalene;;
Other name(s): 8a-epi-α-selinene synthase; NP1
Systematic name: (2Z,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 5-epi-α-selinene-forming)
Comments: Requires Mg2+. The enzyme forms 5-epi-α-selinene possibly via germecrene A or a 1,6-hydride shift mechanism.
References:
1. Agger, S.A., Lopez-Gallego, F., Hoye, T.R. and Schmidt-Dannert, C. Identification of sesquiterpene synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. strain PCC 7120. J. Bacteriol. 190 (2008) 6084-6096. [PMID: 18658271]
EC 4.2.3.91
Accepted name: cubebol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = cubebol + diphosphate
For diagram of reaction click here and mechanism click here.
Other name(s): Cop4
Systematic name: cubebol hydrolase (cyclizing, cubebol-forming)
Comments: Requires Mg2+. The enzyme gives 28% cubebol, 29% (–)-germacrene D, 10% (+)-δ-cadinene and traces of several other sesquiterpenoids. See also EC 4.2.3.75 (–)-germacrene D synthase and EC 4.2.3.13 (+)-δ-cadinene synthase.
References:
1. Lopez-Gallego, F., Agger, S.A., Abate-Pella, D., Distefano, M.D. and Schmidt-Dannert, C. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. Chembiochem. 11 (2010) 1093-1106. [PMID: 20419721]
EC 4.2.3.92
Accepted name: (+)-γ-cadinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-γ-cadinene + diphosphate
For diagram of reaction click here and mechanism click here.
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-γ-cadinene-forming]
Comments: The cloned enzyme from the melon, Cucumis melo, gave mainly δ- and γ-cadinene with traces of several other sesquiterpenoids cf. EC 4.2.3.62 (–)-γ-cadinene synthase [(2Z,6E)-farnesyl diphosphate cyclizing]; EC 4.2.3.13 (+)-δ-cadinene synthase.
References:
1. Iijima, Y., Davidovich-Rikanati, R., Fridman, E., Gang, D.R., Bar, E., Lewinsohn, E. and Pichersky, E. The biochemical and molecular basis for the divergent patterns in the biosynthesis of terpenes and phenylpropenes in the peltate glands of three cultivars of basil. Plant Physiol. 136 (2004) 3724-3736. [PMID: 15516500]
2. Portnoy, V., Benyamini, Y., Bar, E., Harel-Beja, R., Gepstein, S., Giovannoni, J.J., Schaffer, A.A., Burger, J., Tadmor, Y., Lewinsohn, E. and Katzir, N. The molecular and biochemical basis for varietal variation in sesquiterpene content in melon (Cucumis melo L.) rinds. Plant Mol. Biol. 66 (2008) 647-661. [PMID: 18264780]
EC 4.2.3.93
Accepted name: δ-guaiene synthase
Reaction: (2E,6E)-farnesyl diphosphate = δ-guaiene + diphosphate
For diagram of reaction click here.
Glossary: δ-guaiene = α-bulnesene
Systematic name: δ-guaiene hydrolase (cyclizing, δ-guaiene-forming)
Comments: Requires Mg2+. In Aquilaria crassna three clones of the enzyme gave about 80% δ-guaiene and 20% α-guaiene (see also EC 4.2.3.87). A fourth clone gave 54% δ-guaiene and 45% α-guaiene [2]. The enzyme from Pogostemon cablin gives 13% δ-guaiene as well as 37% (–)-patchoulol (see EC 4.2.3.70), 13% α-guaiene (see EC 4.2.3.87), and traces of at least ten other sesquiterpenoids [1].
References:
1. Deguerry, F., Pastore, L., Wu, S., Clark, A., Chappell, J. and Schalk, M. The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Arch. Biochem. Biophys. 454 (2006) 123-136. [PMID: 16970904]
2. Kumeta, Y. and Ito, M. Characterization of δ-guaiene synthases from cultured cells of Aquilaria, responsible for the formation of the sesquiterpenes in agarwood. Plant Physiol. 154 (2010) 1998-2007. [PMID: 20959422]
[EC 5.2.1.3 Deleted entry: retinal isomerase. Now known to be catalysed by a pathway involving EC 1.1.1.300, NADP-retinol dehydrogenase; EC 2.3.1.135, phosphatidylcholineÑretinol O-acyltransferase; EC 3.1.1.64, retinoid isomerohydrolase; and EC 1.1.1.315, 11-cis-retinol dehydrogenase. (EC 5.2.1.3 created 1961, modified 1976, deleted 2011)]
[EC 5.2.1.7 Transferred entry: retinol isomerase. Transferred to EC 3.1.1.64, retinoid isomerohydrolase. (EC 5.2.1.7 created 1989, deleted 2011)]
EC 5.3.2.3
Accepted name: TDP-4-oxo-6-deoxy-α-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-α-D-galactopyranose-forming)
Reaction: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-3-dehydro-6-deoxy-α-D-galactopyranose
Other name(s): dTDP-6-deoxy-hex-4-ulose isomerase; TDP-6-deoxy-hex-4-ulose isomerase; FdtA
Systematic name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose:dTDP-3-dehydro-6-deoxy-α-D-galactopyranose isomerase
Comments: The enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose. Four moieties of α-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-α-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus.
References:
1. Pfoestl, A., Hofinger, A., Kosma, P. and Messner, P. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 278 (2003) 26410-26417. [PMID: 12740380]
2. Davis, M.L., Thoden, J.B. and Holden, H.M. The x-ray structure of dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase. J. Biol. Chem. 282 (2007) 19227-19236. [PMID: 17459872]
EC 5.3.2.4
Accepted name: TDP-4-oxo-6-deoxy-α-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-α-D-glucopyranose-forming)
Reaction: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-3-dehydro-6-deoxy-α-D-glucopyranose
Other name(s): TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase (ambiguous); Tyl1a; dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase (ambiguous)
Systematic name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose:dTDP-3-dehydro-6-deoxy-α-D-glucopyranose isomerase
Comments: The enzyme is involved in biosynthesis of D-mycaminose.
References:
1. Melancon, C.E., 3rd, Hong, L., White, J.A., Liu, Y.N. and Liu, H.W. Characterization of TDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from the D-mycaminose biosynthetic pathway of Streptomyces fradiae: in vitro activity and substrate specificity studies. Biochemistry 46 (2007) 577-590. [PMID: 17209568]
*EC 5.3.3.16
Accepted name: 4-oxalomesaconate tautomerase
Reaction: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate
For diagram of reaction click here.
Glossary: (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = keto tautomer of 4-oxalomesaconate
Other name(s): GalD
Systematic name: 4-oxalomesaconate keto—enol-isomerase
Comments: This enzyme has been characterized from the bacterium Pseudomonas putida KT2440 and is involved in the degradation pathway of syringate and gallate. It catalyses the interconversion of two of the tautomers of 4-oxalomesaconate, a reaction that can also occur spontaneously.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number:
References:
1. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]
EC 5.3.3.18
Accepted name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Reaction: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
Glossary: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-{7-oxabicyclo[4.1.0]hepta-2,4-dien-1-yl}acetyl-CoA
Other name(s): paaG (gene name); 1,2-epoxyphenylacetyl-CoA isomerase (misleading)
Systematic name: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Comments: The enzyme catalyses the reversible isomerization of 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA to the unusual unsaturated, oxygen-containing, seven-member heterocyclic enol ether 2-oxepin-2(3H)-ylideneacetyl-CoA, as part of an aerobic phenylacetate degradation pathway.
References:
1. Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047-3054. [PMID: 12846838]
2. Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390-14395. [PMID: 20660314]
EC 5.4.4.5
Accepted name: 9,12-octadecadienoate 8-hydroperoxide 8R-isomerase
Reaction: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate = (5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate
Glossary: oxepin-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
Other name(s): 5,8-LDS (bifunctional enzyme); 5,8-linoleate diol synthase (bifunctional enzyme); 8-hydroperoxide isomerase; (8R,9Z,12Z)-8-hydroperoxy-9,12-octadecadienoate mutase ((5S,8R,9Z,12Z)-5,8-dihydroxy-9,12-octadecadienoate-forming); PpoA
Systematic name: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate hydroxymutase [(5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate-forming]
Comments: The enzyme contains heme [3]. The bifunctional enzyme from Aspergillus nidulans uses different heme domains to catalyse two separate reactions. Linoleic acid is oxidized within the N-terminal heme peroxidase domain to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate (cf. EC 1.13.11.60, linoleate 8R-lipoxygenase), which is subsequently isomerized to (5S,8R,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate within the C-terminal P450 heme thiolate domain [3].
References:
1. Hoffmann, I., Jerneren, F., Garscha, U. and Oliw, E.H. Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase. Arch. Biochem. Biophys. 506 (2011) 216-222. [PMID: 21130068]
2. Jerneren, F., Garscha, U., Hoffmann, I., Hamberg, M. and Oliw, E.H. Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus. Biochim. Biophys. Acta 1801 (2010) 503-507. [PMID: 20045744]
3. Brodhun, F., Gobel, C., Hornung, E. and Feussner, I. Identification of PpoA from Aspergillus nidulans as a fusion protein of a fatty acid heme dioxygenase/peroxidase and a cytochrome P450. J. Biol. Chem. 284 (2009) 11792-11805. [PMID: 19286665]
EC 5.4.4.6
Accepted name: 9,12-octadecadienoate 8-hydroperoxide 8S-isomerase
Reaction: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate = (7S,8S,9Z,12Z)-7,8-dihydroxyoctadeca-9,12-dienoate
Other name(s): 8-hydroperoxide isomerase (ambiguous); (8R,9Z,12Z)-8-hydroperoxy-9,12-octadecadienoate mutase ((7S,8S,9Z,12Z)-5,8-dihydroxy-9,12-octadecadienoate-forming)
Systematic name: (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate hydroxymutase [(7S,8S,9Z,12Z)-7,8-dihydroxyoctadeca-9,12-dienoate-forming]
Comments: The enzyme contains heme. The bifunctional enzyme from Gaeumannomyces graminis catalyses the oxidation of linoleic acid to (8R,9Z,12Z)-8-hydroperoxyoctadeca-9,12-dienoate (cf. EC 1.13.11.60, linoleate 8R-lipoxygenase), which is then isomerized to (7S,8S,9Z,12Z)-5,8-dihydroxyoctadeca-9,12-dienoate [3].
References:
1. Hamberg, M., Zhang, L.-Y., Brodowsky, I.D. and Oliw, E.H. Sequential oxygenation of linoleic acid in the fungus Gaeumannomyces graminis: stereochemistry of dioxygenase and hydroperoxide isomerase reactions. Arch. Biochem. Biophys. 309 (1994) 77-80. [PMID: 8117115]
2. Su, C., Sahlin, M. and Oliw, E.H. A protein radical and ferryl intermediates are generated by linoleate diol synthase, a ferric hemeprotein with dioxygenase and hydroperoxide isomerase activities. J. Biol. Chem. 273 (1998) 20744-20751. [PMID: 9694817]
3. Su, C. and Oliw, E.H. Purification and characterization of linoleate 8-dioxygenase from the fungus Gaeumannomyces graminis as a novel hemoprotein. J. Biol. Chem. 271 (1996) 14112-14118. [PMID: 8662736]
EC 5.4.99.46
Accepted name: shionone synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = shionone
For diagram of reaction click here.
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, shionone-forming)
Comments: The enzyme gives traces of four other triterpenoids
References:
1. Sawai, S., Uchiyama, H., Mizuno, S., Aoki, T., Akashi, T., Ayabe, S. and Takahashi, T. Molecular characterization of an oxidosqualene cyclase that yields shionone, a unique tetracyclic triterpene ketone of Aster tataricus. FEBS Lett. 585 (2011) 1031-1036. [PMID: 21377465]
EC 5.4.99.47
Accepted name: parkeol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = parkeol
For diagram of reaction click here.
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, parkeol-forming)
Comments: The enzyme from rice (Oryza sativa) produces parkeol as a single product [1].
References:
1. Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678-2681. [PMID: 21526825]
EC 5.4.99.48
Accepted name: achilleol B synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = achilleol B
For diagram of reaction click here.
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, achilleol-B-forming)
Comments: Achilleol B is probably formed by cleavage of the 8-14 and 9-10 bonds of (3S)-2,3-epoxy-2,3-dihydrosqualene as part of the cyclization reaction, after formation of the oleanane skeleton.
References:
1. Ito, R., Mori, K., Hashimoto, I., Nakano, C., Sato, T. and Hoshino, T. Triterpene cyclases from Oryza sativa L.: cycloartenol, parkeol and achilleol B synthases. Org. Lett. 13 (2011) 2678-2681. [PMID: 21526825]
EC 5.4.99.49
Accepted name: glutinol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = glutinol
For diagram of reaction click here.
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, glutinol-forming)
Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.
References:
1. Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703-29712. [PMID: 20610397]
EC 5.4.99.50
Accepted name: friedelin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = friedelin
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, friedelin-forming)
For diagram of reaction click here.
Comments: The enzyme from Kalanchoe daigremontiana also gives traces of other triterpenoids.
References:
1. Wang, Z., Yeats, T., Han, H. and Jetter, R. Cloning and characterization of oxidosqualene cyclases from Kalanchoe daigremontiana: enzymes catalyzing up to 10 rearrangement steps yielding friedelin and other triterpenoids. J. Biol. Chem. 285 (2010) 29703-29712. [PMID: 20610397]
EC 5.4.99.51
Accepted name: baccharis oxide synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = baccharis oxide
For diagram of reaction click here.
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, baccharis-oxide-forming)
Comments: The enzyme from Stevia rebaudiana also gives traces of other triterpenoids.
References:
1. Shibuya, M., Sagara, A., Saitoh, A., Kushiro, T. and Ebizuka, Y. Biosynthesis of baccharis oxide, a triterpene with a 3,10-oxide bridge in the A-ring. Org. Lett. 10 (2008) 5071-5074. [PMID: 18850716]
EC 5.4.99.52
Accepted name: α-seco-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = α-seco-amyrin
For diagram of reaction click here.
Glossary: α-seco-amyrin = 8,14-secoursa-7,13-diene-3β-ol
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, α-seco-amyrin-forming)
Comments: The enzyme from Arabidopsis thaliana is multifunctional and produces about equal amounts of α- and β-seco-amyrin. See EC 5.4.99.54, β-seco-amyrin synthase.
References:
1. Shibuya, M., Xiang, T., Katsube, Y., Otsuka, M., Zhang, H. and Ebizuka, Y. Origin of structural diversity in natural triterpenes: direct synthesis of seco-triterpene skeletons by oxidosqualene cyclase. J. Am. Chem. Soc. 129 (2007) 1450-1455. [PMID: 17263431]
EC 5.4.99.53
Accepted name: marneral synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = marneral
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, marneral-forming)
For diagram of reaction click here.
Comments: Marneral is a triterpenoid formed by Grob fragmentation of the A ring of 2,3-epoxy-2,3-dihydrosqualene during cyclization.
References:
1. Xiong, Q., Wilson, W. K. and Matsuda, S. P. T. An Arabidopsis oxidosqualene cyclase catalyzes iridal skeleton formation by Grob fragmentation. Angew. Chem., Int. Ed. 45 (2006) 1285-1288. [PMID: 16425307]
EC 5.4.99.54
Accepted name: β-seco-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = β-seco-amyrin
For diagram of reaction click here.
Glossary: β-seco-amyrin = 8,14-secooleana-7,13-diene-3β-ol
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, β-seco-amyrin-forming)
Comments: The enzyme from Arabidopsis thaliana is multifunctional and produces about equal amounts of α- and β-seco-amyrin. See EC 5.4.99.52, α-seco-amyrin synthase.
References:
1. Shibuya, M., Xiang, T., Katsube, Y., Otsuka, M., Zhang, H. and Ebizuka, Y. Origin of structural diversity in natural triterpenes: direct synthesis of seco-triterpene skeletons by oxidosqualene cyclase. J. Am. Chem. Soc. 129 (2007) 1450-1455. [PMID: 17263431]
EC 5.4.99.55
Accepted name: δ-amyrin synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = δ-amyrin
For diagram of reaction click here.
Other name(s): SlTTS2 (gene name)
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, δ-amyrin-forming)
Comments: The enzyme from tomato (Solanum lycopersicum) gives 48% δ-amyrin, 18% α-amyrin, 13% β-amyrin and traces of three or four other triterpenoid alcohols [1]. See also EC 5.4.99.40, α-amyrin synthase and EC 5.4.99.39, β-amyrin synthase.
References:
1. Wang, Z., Guhling, O., Yao, R., Li, F., Yeats, T.H., Rose, J.K. and Jetter, R. Two oxidosqualene cyclases responsible for biosynthesis of tomato fruit cuticular triterpenoids. Plant Physiol. 155 (2011) 540-552. [PMID: 21059824]
EC 5.4.99.56
Accepted name: tirucalladienol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = tirucalla-7,24-dien-3β-ol
For diagram of reaction click here.
Other name(s): PEN3
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, tirucalla-7,24-dien-3β-ol-forming)
Comments: The product from Arabidopsis thaliana is 85% tirucalla-7,24-dien-3β-ol with trace amounts of other triterpenoids.
References:
1. Morlacchi, P., Wilson, W.K., Xiong, Q., Bhaduri, A., Sttivend, D., Kolesnikova, M.D. and Matsuda, S.P. Product profile of PEN3: the last unexamined oxidosqualene cyclase in Arabidopsis thaliana. Org. Lett. 11 (2009) 2627-2630. [PMID: 19445469]
EC 5.5.1.20
Accepted name: prosolanapyrone-III cycloisomerase
Reaction: prosolanapyrone III = (–)-solanapyrone A
For diagram of reaction click here
Glossary: prosolanapyrone III = 4-methoxy-2-oxo-6-(1E,7E,9E)-undeca-1,7,9-trienyl-2H-pyran-3-carboxaldehyde
Other name(s): Sol5 (ambiguous); SPS (ambiguos); solanapyrone synthase (bifunctional enzyme: prosolanapyrone II oxidase/prosolanapyrone III cyclosiomerase)
Systematic name: prosolanapyrone-III:(–)-solanapyrone A isomerase
Comments: The enzyme is involved in the biosynthesis of the phytotoxin solanapyrone in some fungi. The bifunctional enzyme catalyses the oxidation of prosolanapyrone II and the subsequent Diels Alder cycloisomerization of the product prosolanapyrone III to (–)-solanapyrone A (cf. EC 1.1.3.42, prosolanapyrone II oxidase).
References:
1. Kasahara, K., Miyamoto, T., Fujimoto, T., Oguri, H., Tokiwano, T., Oikawa, H., Ebizuka, Y. and Fujii, I. Solanapyrone synthase, a possible Diels-Alderase and iterative type I polyketide synthase encoded in a biosynthetic gene cluster from Alternaria solani. Chembiochem. 11 (2010) 1245-1252. [PMID: 20486243]
2. Katayama, K., Kobayashi, T., Oikawa, H., Honma, M. and Ichihara, A. Enzymatic activity and partial purification of solanapyrone synthase: first enzyme catalyzing Diels-Alder reaction. Biochim. Biophys. Acta 1384 (1998) 387-395. [PMID: 9659400]
3. Katayama, K., Kobayashi, T., Chijimatsu, M., Ichihara, A. and Oikawa, H. Purification and N-terminal amino acid sequence of solanapyrone synthase, a natural Diels-Alderase from Alternaria solani. Biosci. Biotechnol. Biochem. 72 (2008) 604-607. [PMID: 18256508]
*EC 6.2.1.2
Accepted name: butyrate—CoA ligase
Reaction: ATP + a carboxylate + CoA = AMP + diphosphate + an acyl-CoA
Other name(s): butyryl-CoA synthetase; fatty acid thiokinase (medium chain); acyl-activating enzyme; fatty acid elongase; fatty acid activating enzyme; fatty acyl coenzyme A synthetase; medium chain acyl-CoA synthetase; butyryl-coenzyme A synthetase; L-(+)-3-hydroxybutyryl CoA ligase; short-chain acyl-CoA synthetase
Systematic name: butanoate:CoA ligase (AMP-forming)
Comments: Acts on acids from C4 to C11 and on the corresponding 3-hydroxy- and 2,3- or 3,4-unsaturated acids.
Links to other databases:
BRENDA,
EXPASY,
GTD,
KEGG,
PDB,
CAS registry number: 9080-51-7
References:
1. Mahler, H.R., Wakil, S.J. and Bock, R.M. Studies on fatty acid oxidation. I. Enzymatic activation of fatty acids. J. Biol. Chem. 204 (1953) 453-468. [PMID: 13084616]
2. Massaro, E.J. and Lennarz, W.J. The partial purification and characterization of a bacterial fatty acyl coenzyme A synthetase. Biochemistry 4 (1965) 85-90. [PMID: 14285249]
3. Websterlt, J.R., Gerowin, L.D. and Rakita, L. Purification and characteristics of a butyryl coenzyme A synthetase from bovine heart mitochondria. J. Biol. Chem. 240 (1965) 29-33. [PMID: 14253428]
*EC 6.2.1.3
Accepted name: long-chain-fatty-acid—CoA ligase
Reaction: ATP + a long-chain carboxylate + CoA = AMP + diphosphate + an acyl-CoA
Other name(s): acyl-CoA synthetase; fatty acid thiokinase (long chain); acyl-activating enzyme; palmitoyl-CoA synthase; lignoceroyl-CoA synthase; arachidonyl-CoA synthetase; acyl coenzyme A synthetase; acyl-CoA ligase; palmitoyl coenzyme A synthetase; thiokinase; palmitoyl-CoA ligase; acyl-coenzyme A ligase; fatty acid CoA ligase; long-chain fatty acyl coenzyme A synthetase; oleoyl-CoA synthetase; stearoyl-CoA synthetase; long chain fatty acyl-CoA synthetase; long-chain acyl CoA synthetase; fatty acid elongase; LCFA synthetase; pristanoyl-CoA synthetase; ACS3; long-chain acyl-CoA synthetase I; long-chain acyl-CoA synthetase II; fatty acyl-coenzyme A synthetase; long-chain acyl-coenzyme A synthetase; FAA1
Systematic name: long-chain fatty acid:CoA ligase (AMP-forming)
Comments: Acts on a wide range of long-chain saturated and unsaturated fatty acids, but the enzymes from different tissues show some variation in specificity. The liver enzyme acts on acids from C6 to C20; that from brain shows high activity up to C24.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
UM-BBD,
CAS registry number: 9013-18-7
References:
1. Bakken, A.M. and Farstad, M. Identical subcellular distribution of palmitoyl-CoA and arachidonoyl-CoA synthetase activities in human blood platelets. Biochem. J. 261 (1989) 71-76. [PMID: 2528345]
2. Hosaka, K., Mishima, M., Tanaka, T., Kamiryo, T. and Numa, S. Acyl-coenzyme-A synthetase I from Candida lipolytica. Purification, properties and immunochemical studies. Eur. J. Biochem. 93 (1979) 197-203. [PMID: 108099]
3. Nagamatsu, K., Soeda, S., Mori, M. and Kishimoto, Y. Lignoceroyl-coenzyme A synthetase from developing rat brain: partial purification, characterization and comparison with palmitoyl-coenzyme A synthetase activity and liver enzyme. Biochim. Biophys. Acta 836 (1985) 80-88. [PMID: 3161545]
4. Tanaka, T., Hosaka, K., Hoshimaru, M. and Numa, S. Purification and properties of long-chain acyl-coenzyme-A synthetase from rat liver. Eur. J. Biochem. 98 (1979) 165-172. [PMID: 467438]
*EC 6.2.1.10
Accepted name: acid—CoA ligase (GDP-forming)
Reaction: GTP + a carboxylate + CoA = GDP + phosphate + acyl-CoA
Other name(s): acyl-CoA synthetase (GDP-forming); acyl coenzyme A synthetase (guanosine diphosphate forming)
Systematic name: acid:CoA ligase (GDP-forming)
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37318-59-5
References:
1. Rossi, C.R. and Gibson, D.M. Activation of fatty acids by a guanosine triphosphate-specific thiokinase from liver mitochondria. J. Biol. Chem. 239 (1964) 1694-1699. [PMID: 14213337]
*EC 6.2.1.19
Accepted name: long-chain-fatty-acid—luciferin-component ligase
Reaction: ATP + a carboxylate + protein = AMP + diphosphate + an acyl-protein thioester
Other name(s): acyl-protein synthetase
Systematic name: long-chain-fatty-acid:protein ligase (AMP-forming)
Comments: Together with EC 1.2.1.50 long-chain-fatty-acyl-CoA reductase, enzyme forms a fatty acid reductase system that produces the substrate of EC 1.14.14.3 alkanal monooxygenase (FMN-linked), thus being a component of the bacterial luciferase system.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
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. Wall, L. and Meighen, E.A. Subunit structure of the fatty-acid reductase complex from Photobacterium phosphoreum. Biochemistry 25 (1986) 4315-4321.
*EC 6.2.1.23
Accepted name: dicarboxylate—CoA ligase
Reaction: ATP + an α,ω-dicarboxylate + CoA = AMP + diphosphate + an ω-carboxyacyl-CoA
Other name(s): carboxylyl-CoA synthetase; dicarboxylyl-CoA synthetase
Systematic name: ω-dicarboxylate:CoA ligase (AMP-forming)
Comments: Acts on dicarboxylic acids of chain length C5 to C16; the best substrate is dodecanedioic acid.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 99332-77-1
References:
1. Vamecq, J., de Hoffmann, E. and van Hoof, F. The microsomal dicarboxylyl-CoA synthetase. Biochem. J. 230 (1985) 683-693. [PMID: 4062873]
perakine = raucaffrine = (17R,20α,21β)-1,2-didehydro-1-demethyl-17-(acetyloxy)-21-methyl-18-norajmalan-19-al
prosolanapyrone III = 4-methoxy-2-oxo-6-(1E,7E,9E)-undeca-1,7,9-trien-1-yl-2H-pyran-3-carboxaldehyde
(1a) 15-cis-4,4'-diapophytoene + FAD = all-trans-4,4'-diapophytofluene + FADH2
(1b) all-trans-4,4'-diapophytofluene + FAD = all-trans-4,4'-diapo-ζ-carotene + FADH2
(1c) all-trans-4,4'-diapo-ζ-carotene + FAD = all-trans-4,4'-diapolneurosporene + FADH2
(1d) all-trans-4,4'-diaponeurosporene + FAD = all-trans-4,4'-diapolycopene + FADH2
α-linolenate = (9Z,12Z,15Z)-octadeca-9,12,15-trienoate
(1a) pentalenene + NADPH + H+ + O2 = pentalen-13-ol + NADP+ + H2O
(1b) pentalen-13-ol + NADPH + H+ + O2 = pentalen-13-al + NADP+ + 2 H2O
(1a) β-amyrin + O2 + NADPH + H+ = 11α-hydroxy-β-amyrin + H2O + NADP+
(1b) 11α-hydroxy-β-amyrin + O2 + NADPH + H+ = 11-oxo-β-amyrin + 2 H2O + NADP+
T = ribothymidine = 5-methyluridine
dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose = dTDP-D-desosamine
mycinamicin IV = [(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-2,3-di-O-methyl-β-D-allopyranoside
mycinamicin VI = [(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-β-D-allopyranoside
cPMP = cyclic pyranopterin monophosphate = precursor Z = 8-amino-2,12,12-trihydroxy-4a,5a,6,9,11,11a,12,12a-octahydro[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridin-10(4H)-one 2-oxide = 8-amino-2,12,12-trihydroxy-4,4a,5a,6,9,10,11,11a,12,12a-decahydro-[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridine 2-oxide
phosphatidylinositol-3,4,5-trisphosphate = PtdIns(3,4,5)P3
phosphatidylinositol-1,3,4,5-trisphosphate = PtdIns(1,3,4,5)P4
or Lys-Gly, to release flagellin.
(2) a D-glucosyl-N-acylsphingosine + H2O = a fatty acid + D-glucosyl-sphingosine
D-glucosyl-N-acylsphingosine = glucosylceramide
(2) thiamine + H2O = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole
[= 8a-epi-α-selinene which uses naththalene numbering not eudesmane]
(1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricaboxylate = one of the enol tautomers of 4-oxalomesaconate
(–)-solanapyrone A = 4-methoxy-6-((1R,2S,4aR,8aR)-2-methyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl)-2-oxo-2H-pyran-3-carboxaldehyde
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