An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: (R)-3-hydroxyacid-ester dehydrogenase
Reaction: ethyl (R)-3-hydroxyhexanoate + NADP+ = ethyl 3-oxohexanoate + NADPH + H+
Other name(s): 3-oxo ester (R)-reductase
Systematic name: ethyl-(R)-3-hydroxyhexanoate:NADP+ 3-oxidoreductase
Comments: Also acts on ethyl (R)-3-oxobutanoate and some other (R)-3-hydroxy acid esters. The (R)- symbol is allotted on the assumption that no substituents change the order of priority from O-3 > C-2 > C-4. A subunit of yeast fatty acid synthase EC 2.3.1.86, fatty-acyl-CoA synthase system. cf. EC 1.1.1.280, (S)-3-hydroxyacid ester dehydrogenase.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 114705-02-1
References:
1. Heidlas, J., Engel, K.-H. and Tressl, R. Purification and characterization of two oxidoreductases involved in the enantioselective reduction of 3-oxo, 4-oxo and 5-oxo esters in baker's yeast. Eur. J. Biochem. 172 (1988) 633-639. [PMID: 3280313]
Accepted name: isopyridoxal dehydrogenase (5-pyridoxolactone-forming)
Reaction: isopyridoxal + NAD+ = 5-pyridoxolactone + NADH + H+
Glossary: isopyridoxal = 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carbaldehyde
5-pyridoxolactone = 7-hydroxy-6-methylfuro[3,4-c]pyridin-3(1H)-one
Systematic name: isopyridoxal:NAD+ oxidoreductase (5-pyridoxolactone-forming)
Comments: The enzyme, characterized from the bacterium Arthrobacter sp. Cr-7, participates in the degradation of pyridoxine. The enzyme also catalyses the activity of EC 1.2.1.102, isopyridoxal dehydrogenase (5-pyridoxate-forming).
References:
1. Lee, Y.C., Nelson, M.J. and Snell, E.E. Enzymes of vitamin B6 degradation. Purification and properties of isopyridoxal dehydrogenase and 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid dehydrogenase. J. Biol. Chem 261 (1986) 15106-15111. [PMID: 3533936]
Accepted name: isopyridoxal dehydrogenase (5-pyridoxate-forming)
Reaction: isopyridoxal + NAD+ + H2O = 5-pyridoxate + NADH + H+
Glossary: isopyridoxal = 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carbaldehyde
5-pyridoxate = 3-hydroxy-4-hydroxymethyl-2-methylpyridine-5-carboxylate
Systematic name: isopyridoxal:NAD+ oxidoreductase (5-pyridoxate-forming)
Comments: The enzyme, characterized from the bacterium Arthrobacter sp. Cr-7, participates in the degradation of pyridoxine. The enzyme also catalyses the activity of EC 1.1.1.416, isopyridoxal dehydrogenase (5-pyridoxolactone-forming).
References:
1. Lee, Y.C., Nelson, M.J. and Snell, E.E. Enzymes of vitamin B6 degradation. Purification and properties of isopyridoxal dehydrogenase and 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid dehydrogenase. J. Biol. Chem 261 (1986) 15106-15111. [PMID: 3533936]
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific)
Reaction: an acyl-[acyl-carrier protein] + NADP+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH + H+
Other name(s): acyl-ACP dehydrogenase (ambiguous); enoyl-[acyl carrier protein] (reduced nicotinamide adenine dinucleotide phosphate) reductase; NADPH 2-enoyl Co A reductase; enoyl acyl-carrier-protein reductase (ambiguous); enoyl-ACP reductase (ambiguous); acyl-[acyl-carrier-protein]:NADP+ oxidoreductase (B-specific); acyl-[acyl-carrier protein]:NADP+ oxidoreductase (B-specific); enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific)
Systematic name: acyl-[acyl-carrier protein]:NADP+ oxidoreductase (Si-specific)
Comments: One of the activities of EC 2.3.1.86, fatty-acyl-CoA synthase system, an enzyme found in yeasts (Ascomycota and Basidiomycota). Catalyses the reduction of enoyl-acyl-[acyl-carrier protein] derivatives of carbon chain length from 4 to 16. The yeast enzyme is Si-specific with respect to NADP+. cf. EC 1.3.1.39, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) and EC 1.3.1.104, enoyl-[acyl-carrier-protein] reductase (NADPH), which describes enzymes whose stereo-specificity towards NADPH is not known. See also EC 1.3.1.9, enoyl-[acyl-carrier-protein] reductase (NADH).
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number: 37251-09-5
References:
1. Seyama, T., Kasama, T., Yamakawa, T., Kawaguchi, A., Saito, K. and Okuda, S. Origin of hydrogen atoms in the fatty acids synthesized with yeast fatty acid synthetase. J. Biochem. (Tokyo) 82 (1977) 1325-1329. [PMID: 338601]
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
Reaction: an acyl-[acyl-carrier protein] + NADP+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH + H+
Other name(s): acyl-ACP dehydrogenase; enoyl-[acyl carrier protein] (reduced nicotinamide adenine dinucleotide phosphate) reductase; NADPH 2-enoyl Co A reductase; enoyl-ACp reductase; enoyl-[acyl-carrier-protein] reductase (NADPH2, A-specific); acyl-[acyl-carrier-protein]:NADP+ oxidoreductase (A-specific); enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific); acyl-[acyl-carrier protein]:NADP+ oxidoreductase (A-specific)
Systematic name: acyl-[acyl-carrier protein]:NADP+ oxidoreductase (Re-specific)
Comments: This enzyme completes each cycle of fatty acid elongation by catalysing the stereospecific reduction of the double bond at position 2 of a growing fatty acid chain, while linked to an acyl-carrier protein. It is one of the activities of EC 2.3.1.85, fatty-acid synthase system. The mammalian enzyme is Re-specific with respect to NADP+. cf. EC 1.3.1.10, enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific) and EC 1.3.1.104, enoyl-[acyl-carrier-protein] reductase (NADPH).
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Dugan, R.E., Slakey, L.L. and Porter, L.W. Stereospecificity of the transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate to the acyl chain in the dehydrogenase-catalyzed reactions of fatty acid synthesis. J. Biol. Chem. 245 (1970) 6312-6316. [PMID: 4394955]
2. Carlisle-Moore, L., Gordon, C.R., Machutta, C.A., Miller, W.T. and Tonge, P.J. Substrate recognition by the human fatty-acid synthase. J. Biol. Chem. 280 (2005) 42612-42618. [PMID: 16215233]
Accepted name: trimethylamine-N-oxide reductase
Reaction: trimethylamine + 2 (ferricytochrome c)-subunit + H2O = trimethylamine N-oxide + 2 (ferrocytochrome c)-subunit + 2 H+
For diagram of reaction click here
Other name(s): TMAO reductase; TOR; torA (gene name); torZ (gene name); bisZ (gene name); trimethylamine-N-oxide reductase (cytochrome c)
Systematic name: trimethylamine:cytochrome c oxidoreductase
Comments: Contains bis(molybdopterin guanine dinucleotide)molybdenum cofactor. The reductant is a membrane-bound multiheme cytochrome c. Also reduces dimethyl sulfoxide to dimethyl sulfide.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number: 37256-34-1
References:
1. Arata, H., Shimizu, M. and Takamiya, K. Purification and properties of trimethylamine N-oxide reductase from aerobic photosynthetic bacterium Roseobacter denitrificans. J. Biochem. (Tokyo) 112 (1992) 470-475. [PMID: 1337081]
2. Knablein, J., Dobbek, H., Ehlert, S. and Schneider, F. Isolation, cloning, sequence analysis and X-ray structure of dimethyl sulfoxide trimethylamine N-oxide reductase from Rhodobacter capsulatus. Biol. Chem. 378 (1997) 293-302. [PMID: 9165084]
3. Czjzek, M., Dos Santos, J.P., Pommier, J., Giordano, G., Méjean, V. and Haser, R. Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 Å resolution. J. Mol. Biol. 284 (1998) 435-447. [PMID: 9813128]
4. Gon, S., Giudici-Orticoni, M.T., Mejean, V. and Iobbi-Nivol, C. Electron transfer and binding of the c-type cytochrome TorC to the trimethylamine N-oxide reductase in Escherichia coli. J. Biol. Chem. 276 (2001) 11545-11551. [PMID: 11056172]
5. Zhang, L., Nelson, K.J., Rajagopalan, K.V. and George, G.N. Structure of the molybdenum site of Escherichia coli trimethylamine N-oxide reductase. Inorg. Chem. 47 (2008) 1074-1078. [PMID: 18163615]
6. Yin, Q.J., Zhang, W.J., Qi, X.Q., Zhang, S.D., Jiang, T., Li, X.G., Chen, Y., Santini, C.L., Zhou, H., Chou, I.M. and Wu, L.F. High hydrostatic pressure inducible trimethylamine N-oxide reductase improves the pressure tolerance of piezosensitive bacteria Vibrio fluvialis. Front Microbiol 8 (2017) 2646. [PMID: 29375513]
Accepted name: 7-deoxyloganate 7-hydroxylase
Reaction: 7-deoxyloganate + [reduced NADPH—hemoprotein reductase] + O2 = loganate + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of reaction click here
Glossary: logonate = (1S,4aS,6S,7R,7aS)-1-(β-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylate
Other name(s): CYP72A224 (gene name); 7-deoxyloganin 7-hydroxylase (incorrect); 7-deoxyloganin,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (7α-hydroxylating) (incorrect)
Systematic name: 7-deoxyloganate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (7α-hydroxylating)
Comments: The enzyme, characterized from the plant Catharanthus roseus, is a cytochrome P-450 (heme-thiolate) enzyme. It catalyses a reaction in the pathway leading to biosynthesis of monoterpenoid indole alkaloids.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 335305-40-3
References:
1. Katano, N., Yamamoto, H., Iio, R. and Inoue, K. 7-Deoxyloganin 7-hydroxylase in Lonicera japonica cell cultures. Phytochemistry 58 (2001) 53-58. [PMID: 11524113]
2. Miettinen, K., Dong, L., Navrot, N., Schneider, T., Burlat, V., Pollier, J., Woittiez, L., van der Krol, S., Lugan, R., Ilc, T., Verpoorte, R., Oksman-Caldentey, K.M., Martinoia, E., Bouwmeester, H., Goossens, A., Memelink, J. and Werck-Reichhart, D. The seco-iridoid pathway from Catharanthus roseus. Nat Commun 5 (2014) 3606. [PMID: 24710322]
Accepted name: (S)-N-methylcanadine 1-hydroxylase
Reaction: (S)-N-methylcanadine + [reduced NADPH—hemoprotein reductase] + O2 = (S)-1-hydroxy-N-methylcanadine + [oxidized NADPH—hemoprotein reductase] + H2O
Other name(s): CYP82Y1 (gene name)
Systematic name: (S)-N-methylcanadine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (1-hydroxylating)
Comments: This cytochrome P-450 (heme-thiolate) enzyme, characterized from the plant Papaver somniferum (opium poppy), participates in the biosynthesis of the isoquinoline alkaloid noscapine.
References:
1. Dang, T.T. and Facchini, P.J. CYP82Y1 is N-methylcanadine 1-hydroxylase, a key noscapine biosynthetic enzyme in opium poppy. J. Biol. Chem 289 (2014) 2013-2026. [PMID: 24324259]
2. Li, Y., Li, S., Thodey, K., Trenchard, I., Cravens, A. and Smolke, C.D. Complete biosynthesis of noscapine and halogenated alkaloids in yeast. Proc. Natl Acad. Sci. USA 115 (2018) E3922-E3931. [PMID: 29610307]
Accepted name: (13S,14R)-13-O-acetyl-1-hydroxy-N-methylcanadine 8-hydroxylase
Reaction: (13S,14R)-13-O-acetyl-1-hydroxy-N-methylcanadine + [reduced NADPH—hemoprotein reductase] + O2 = (13S,14R)-13-O-acetyl-1,8-dihydroxy-N-methylcanadine + [oxidized NADPH—hemoprotein reductase] + H2O
Other name(s): CYP82X1 (gene name)
Systematic name: (13S,14R)-13-O-acetyl-1-hydroxy-N-methylcanadine 8-hydroxylase,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (8-hydroxylating)
Comments: This cytochrome P-450 (heme-thiolate) enzyme, characterized from the plant Papaver somniferum (opium poppy), participates in the biosynthesis of the isoquinoline alkaloid noscapine.
References:
1. Dang, T.T., Chen, X. and Facchini, P.J. Acetylation serves as a protective group in noscapine biosynthesis in opium poppy. Nat. Chem. Biol. 11 (2015) 104-106. [PMID: 25485687]
2. Li, Y. and Smolke, C.D. Engineering biosynthesis of the anticancer alkaloid noscapine in yeast. Nat Commun 7 (2016) 12137. [PMID: 27378283]
3. Li, Y., Li, S., Thodey, K., Trenchard, I., Cravens, A. and Smolke, C.D. Complete biosynthesis of noscapine and halogenated alkaloids in yeast. Proc. Natl Acad. Sci. USA 115 (2018) E3922-E3931. [PMID: 29610307]
Accepted name: germacrene A acid 8β-hydroxylase
Reaction: germacra-1(10),4,11(13)-trien-12-oate + [reduced NADPH—hemoprotein reductase] + O2 = 8β-hydroxygermacra-1(10),4,11(13)-trien-12-oate + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of reaction click here.
Glossary: germacra-1(10),4,11(13)-trien-12-oate = germacrene A acid
8β-hydroxygermacra-1(10),4,11(13)-triene-12-oate = 8β-hydroxygermacrene A acid
inunolide = germacra-1(10),4,11(13)-trien-12,8β-lactone
8-epi-inunolide = germacra-1(10),4,11(13)-trien-12,8α-lactone
Other name(s): HaG8H; CYP71BL1; CYP71BL6
Systematic name: germacra-1(10),4,11(13)-trien-12-oate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (8β-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein from the plant Helianthus annuus (common sunflower). The cyclisation of 8β-hydroxygermacra-1(10),4,11(13)-triene-12-oate to inunolide (12,8β) does not seem to occur spontaneously. The enzyme from Inula hupehensis also forms some 8α-hydroxygermacra-1(10),4,11(13)-triene-12-oate, which spontaneously cyclises to 8-epi-inunolide (12,8α) (cf. EC 1.14.14.170 8-epi-inunolide synthase).
References:
1. Frey, M., Schmauder, K., Pateraki, I. and Spring, O. Biosynthesis of eupatolide-A metabolic route for sesquiterpene lactone formation involving the P450 enzyme CYP71DD6. ACS Chem. Biol. 13 (2018) 1536-1543. [PMID: 29758164]
2. Gou, J., Hao, F., Huang, C., Kwon, M., Chen, F., Li, C., Liu, C., Ro, D.K., Tang, H. and Zhang, Y. Discovery of a non-stereoselective cytochrome P450 catalyzing either 8α- or 8β-hydroxylation of germacrene A acid from the Chinese medicinal plant, Inula hupehensis. Plant J. 93 (2018) 92-106. [PMID: 29086444]
Accepted name: eupatolide synthase
Reaction: 8β-hydroxygermacra-1(10),4,11(13)-trien-12-oate + [reduced NADPH—hemoprotein reductase] + O2 = eupatolide + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) 8β-hydroxygermacra-1(10),4,11(13)-trien-12-oate + [reduced NADPH—hemoprotein reductase] + O2 = 6α,8β-dihydroxygermacra-1(10),4,11(13)-trien-12-oate + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) 6α,8β-dihydroxygermacra-1(10),4,11(13)-trien-12-oate = eupatolide + H2O (spontaneous)
For diagram of reaction click here.
Glossary: 8β-hydroxygermacra-1(10),4,11(13)-triene-12-oate = 8β-hydroxygermacrene A acid
eupatolide = 8β-hydroxygermacra-1(10),4,11(13)-trien-12,6α-lactone
Other name(s): CYP71DD6; HaES
Systematic name: 8β-hydroxygermacra-1(10),4,11(13)-trien-12-oate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (6α-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein from the plant Helianthus annuus (common sunflower).
References:
1. Frey, M., Schmauder, K., Pateraki, I. and Spring, O. Biosynthesis of eupatolide-A metabolic route for sesquiterpene lactone formation involving the P450 enzyme CYP71DD6. ACS Chem. Biol. 13 (2018) 1536-1543. [PMID: 29758164]
Accepted name: 8-epi-inunolide synthase
Reaction: germacra-1(10),4,11(13)-trien-12-oate + [reduced NADPH—hemoprotein reductase] + O2 = 8-epi-inunolide + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) germacra-1(10),4,11(13)-trien-12-oate + [reduced NADPH—hemoprotein reductase] + O2 = 8α-hydroxygermacra-1(10),4,11(13)-trien-12-oate + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) 8α-hydroxygermacra-1(10),4,11(13)-trien-12-oate = 8-epi-inunolide + H2O (spontaneous)
Glossary: 8-epi-inunolide = germacra-1(10),4,11(13)-trien-12,8α-lactone
Other name(s): CYP71BL1
Systematic name: germacra-1(10),4,11(13)-trien-12-oate,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (8α-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein from the plant Inula hupehensis. The enzyme also produces 8β-hydroxygermacra-1(10),4,11(13)-triene-12-oate (EC 1.14.14.168, germacrene A acid 8β-hydroxylase).
References:
1. Gou, J., Hao, F., Huang, C., Kwon, M., Chen, F., Li, C., Liu, C., Ro, D.K., Tang, H. and Zhang, Y. Discovery of a non-stereoselective cytochrome P450 catalyzing either 8α- or 8β-hydroxylation of germacrene A acid from the Chinese medicinal plant, Inula hupehensis. Plant J. 93 (2018) 92-106. [PMID: 29086444]
Accepted name: flavone synthase II
Reaction: a flavanone + [reduced NADPH—hemoprotein reductase] + O2 = a flavone + [oxidized NADPH—hemoprotein reductase] + 2 H2O
For diagram of reaction click here.
Other name(s): CYP93B16 (gene name); CYP93G1 (gene name); FNS II
Systematic name: flavanone,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (flavone-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein found in plants. The rice enzyme channels flavanones to the biosynthesis of tricin O-linked conjugates. cf. EC 1.14.20.5, flavone synthase I.
References:
1. Martens, S. and Forkmann, G. Cloning and expression of flavone synthase II from Gerbera hybrids. Plant J. 20 (1999) 611-618. [PMID: 10652133]
2. Fliegmann, J., Furtwangler, K., Malterer, G., Cantarello, C., Schuler, G., Ebel, J. and Mithofer, A. Flavone synthase II (CYP93B16) from soybean (Glycine max L.). Phytochemistry 71 (2010) 508-514. [PMID: 20132953]
3. Lam, P.Y., Zhu, F.Y., Chan, W.L., Liu, H. and Lo, C. Cytochrome P450 93G1 is a flavone synthase II that channels flavanones to the biosynthesis of tricin O-linked conjugates in rice. Plant Physiol. 165 (2014) 1315-1327. [PMID: 24843076]
Accepted name: cyanocobalamin reductase (cyanide-eliminating)
Reaction: 2 cob(II)alamin-[cyanocobalamin reductase] + 2 hydrogen cyanide + NADP+ = 2 cyanocob(III)alamin + 2 [cyanocobalamin reductase] + NADPH + H+
Other name(s): MMACHC (gene name); CblC; cyanocobalamin reductase; cyanocobalamin reductase (NADPH, cyanide-eliminating); cyanocobalamin reductase (NADPH; CN-eliminating); NADPH:cyanocob(III)alamin oxidoreductase (cyanide-eliminating); cob(I)alamin, cyanide:NADP+ oxidoreductase
Systematic name: cob(II)alamin, hydrogen cyanide:NADP+ oxidoreductase
Comments: The mammalian enzyme, which is cytosolic, can bind internalized cyanocobalamin and process it to cob(II)alamin by removing the upper axial ligand. The product remains bound to the protein, which, together with its interacting partner MMADHC, transfers it directly to downstream enzymes involved in adenosylcobalamin and methylcobalamin biosynthesis. In addition to its decyanase function, the mammalian enzyme also catalyses an entirely different chemical reaction with alkylcobalamins, using the thiolate of glutathione for nucleophilic displacement, generating cob(I)alamin and the corresponding glutathione thioether (cf. EC 2.5.1.151, alkylcobalamin dealkylase).
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 131145-00-1
References:
1. Watanabe, F., Oki, Y., Nakano, Y. and Kitaoka, S. Occurrence and characterization of cyanocobalamin reductase (NADPH; CN-eliminating) involved in decyanation of cyanocobalamin in Euglena gracilis. J. Nutr. Sci. Vitaminol. 34 (1988) 1-10. [PMID: 3134526]
2. Kim, J., Gherasim, C. and Banerjee, R. Decyanation of vitamin B12 by a trafficking chaperone. Proc. Natl Acad. Sci. USA 105 (2008) 14551-14554. [PMID: 18779575]
3. Koutmos, M., Gherasim, C., Smith, J.L. and Banerjee, R. Structural basis of multifunctionality in a vitamin B12-processing enzyme. J. Biol. Chem. 286 (2011) 29780-29787. [PMID: 21697092]
4. Mah, W., Deme, J.C., Watkins, D., Fung, S., Janer, A., Shoubridge, E.A., Rosenblatt, D.S. and Coulton, J.W. Subcellular location of MMACHC and MMADHC, two human proteins central to intracellular vitamin B12 metabolism. Mol Genet Metab 108 (2013) 112-118. [PMID: 23270877]
Accepted name: D-proline reductase
Reaction: 5-aminopentanoate + a [PrdC protein with a selenide-sulfide bridge] = D-proline + a [PrdC protein with thiol/selenol residues]
For diagram of reaction mechanism click here
Other name(s): prdAB (gene names); D-proline reductase (dithiol)
Systematic name: 5-aminopentanoate:[PrdC protein] oxidoreductase (cyclizing)
Comments: A pyruvoyl- and L-selenocysteine-containing enzyme found in a number of Clostridial species. The pyruvoyl group, located on the PrdA subunit, binds the substrate, while the selenocysteine residue, located on the PrdB subunit, attacks the α-C-atom of D-proline, leading to a reductive cleavage of the C-N-bond of the pyrrolidine ring and formation of a selenoether. The selenoether is cleaved by a cysteine residue of PrdB, resulting in a mixed selenide-sulfide bridge, which is restored to its reduced state by another selenocysteine protein, PrdC. 5-aminopentanoate is released from PrdA by hydrolysis, regenerating the pyruvoyl moiety. The resulting mixed selenide-sulfide bridge in PrdC is reduced by NADH.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 37255-43-9
References:
1. Stadtman, T.C. and Elliott, P. Studies on the enzymic reduction of amino acids. II. Purification and properties of a D-proline reductase and a proline racemase from Clostridium sticklandii. J. Biol. Chem. 228 (1957) 983-997. [PMID: 13475375]
2. Hodgins, D.S. and Abeles, R.H. Studies of the mechanism of action of D-proline reductase: the presence on covalently bound pyruvate and its role in the catalytic process. Arch. Biochem. Biophys. 130 (1969) 274-285. [PMID: 5778643]
3. Kabisch, U.C., Gräntzdörffer, A., Schierhorn, A., Rücknagel, K.P, Andreesen, J.R. and Pich, A. Identification of D-proline reductase from Clostridium sticklandii as a selenoenzyme and indications for a catalytically active pyruvoyl group derived from a cysteine residue by cleavage of a proprotein. J. Biol. Chem. 274 (1999) 8445-8454. [PMID: 10085076]
4. Bednarski, B., Andreesen, J.R. and Pich, A. In vitro processing of the proproteins GrdE of protein B of glycine reductase and PrdA of D-proline reductase from Clostridium sticklandii: formation of a pyruvoyl group from a cysteine residue. Eur. J. Biochem. 268 (2001) 3538-3544. [PMID: 11422384]
5. Fonknechten, N., Chaussonnerie, S., Tricot, S., Lajus, A., Andreesen, J.R., Perchat, N., Pelletier, E., Gouyvenoux, M., Barbe, V., Salanoubat, M., Le Paslier, D., Weissenbach, J., Cohen, G.N. and Kreimeyer, A. Clostridium sticklandii, a specialist in amino acid degradation: revisiting its metabolism through its genome sequence. BMC Genomics 11 (2010) 555. [PMID: 20937090]
Accepted name: tetrachlorohydroquinone reductive dehalogenase
Reaction: (1) 2,6-dichlorohydroquinone + Cl- + glutathione disulfide = 2,3,6-trichlorohydroquinone + 2 glutathione
(2) 2,3,6-trichlorohydroquinone + Cl- + glutathione disulfide = 2,3,5,6-tetrachlorohydroquinone + 2 glutathione
Other name(s): pcpC (gene name)
Systematic name: glutathione disulfide:2,6-dichlorohydroquinone (chlorinating)
Comments: The enzyme, characterized from the bacterium Sphingobium chlorophenolicum, converts tetrachlorohydroquinone to 2,6-dichlorohydroquinone in two steps, via 2,3,6-trichlorohydroquinone, using glutathione as the reducing agent. The enzyme is sensitive to oxidation - when an internal L-cysteine residue is oxidized, the enzyme produces 2,3,5-trichloro-6-(glutathion-S-yl)-hydroquinone and 2,6-dichloro-3-(glutathion-S-yl)-hydroquinone instead of its normal products.
References:
1. Xun, L., Topp, E. and Orser, C.S. Purification and characterization of a tetrachloro-p-hydroquinone reductive dehalogenase from a Flavobacterium sp. J. Bacteriol. 174 (1992) 8003-8007. [PMID: 1459949]
2. McCarthy, D.L., Navarrete, S., Willett, W.S., Babbitt, P.C. and Copley, S.D. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry 35 (1996) 14634-14642. [PMID: 8931562]
Accepted name: xanthohumol 4-O-methyltransferase
Reaction: S-adenosyl-L-methionine + xanthohumol = S-adenosyl-L-homocysteine + 4-O-methylxanthohumol
For diagram of reaction click here
Glossary: xanthohumol = 2',4,4'-trihydroxy-6'-methoxy-3-prenylchalcone = (2E)-1-[2,4-dihydroxy-6-methoxy-3-(3-methylbut-2-en-1-yl)phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one
4-O-methylxanthohumol =2',4'-dihydroxy-4,6'-dimethoxy-3-prenylchalcone = (2E)-1-[2,4-dihydroxy-6-methoxy-3-(3-methylbut-2-en-1-yl)phenyl]-3-(4-methoxyphenyl)prop-2-en-1-one
Other name(s): OMT2 (ambiguous); S-adenosyl-L-methionine:xanthohumol 4'-O-methyltransferase (incorrect); xanthohumol 4'-O-methyltransferase (incorrect)
Systematic name: S-adenosyl-L-methionine:xanthohumol 4-O-methyltransferase
Comments: The enzyme from hops (Humulus lupulus) has a broad substrate specificity. The best substrates in vitro are resveratrol, desmethylxanthohumol, naringenin chalcone and isoliquiritigenin.
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Nagel, J., Culley, L.K., Lu, Y., Liu, E., Matthews, P.D., Stevens, J.F. and Page, J.E. EST analysis of hop glandular trichomes identifies an O-methyltransferase that catalyzes the biosynthesis of xanthohumol. Plant Cell 20 (2008) 186-200. [PMID: 18223037]
Accepted name: nocamycin O-methyltransferase
Reaction: S-adenosyl-L-methionine + nocamycin E = S-adenosyl-L-homocysteine + nocamycin I
For diagram of reaction click here
Glossary: nocamycin E = (2R,3S,3aS,5R,6R,7S,9aS)-5-[(2R,3E,5E)-7-hydroxy-4-methyl-7-(2,4-dioxopyrroliden-3-ylidene)hepta-3,5-dien-2-yl]-2,6,9a-trimethyl-8-oxooctahydro-3a,7-epoxyfuro[3,2-b]oxocine-3-carboxylate
nocamycin I = methyl (2R,3S,3aS,5R,6R,7S,9aS)-5-[(2R,3E,5E)-7-hydroxy-4-methyl-7-(2,4-dioxopyrroliden-3-ylidene)hepta-3,5-dien-2-yl]-2,6,9a-trimethyl-8-oxooctahydro-3a,7-epoxyfuro[3,2-b]oxocine-3-carboxylate
Other name(s): ncmP (gene name)
Systematic name: S-adenosyl-L-methionine:nocamycin E O-methyltransferase
Comments: The enzyme, isolated from the bacterium Saccharothrix syringae, is involved in the biosynthesis of nocamycin I and nocamycin II.
References:
1. Mo, X., Gui, C. and Wang, Q. Elucidation of a carboxylate O-methyltransferase NcmP in nocamycin biosynthetic pathway. Bioorg. Med. Chem. Lett. 27 (2017) 4431-4435. [PMID: 28818448]
Accepted name: 3-O-acetyl-4'-O-demethylpapaveroxine 4'-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-O-acetyl-4'-O-demethylpapaveroxine = S-adenosyl-L-homocysteine + 3-O-acetylpapaveroxine
Glossary: 3-O-acetyl-4'-O-demethylpapaveroxine = 6-{(S)-acetoxy[(5R)-4-hydroxy-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]methyl}-2,3-dimethoxybenzaldehyde
3-O-acetylpapaveroxine = 6-{(S)-acetoxy[(5R)-4-methoxy-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]methyl}-2,3-dimethoxybenzaldehyde
Systematic name: S-adenosyl-L-methionine:3-O-acetyl-4'-O-demethylpapaveroxine 4'-O-methyltransferase
Comments: This activity is part of the noscapine biosynthesis pathway, as characterized in the plant Papaver somniferum (opium poppy). It is catalysed by heterodimeric complexes of the OMT2 gene product and the product of either OMT3 or 6OMT. OMT2 is the catalytic subunit in both complexes.
References:
1. Li, Y. and Smolke, C.D. Engineering biosynthesis of the anticancer alkaloid noscapine in yeast. Nat Commun 7 (2016) 12137. [PMID: 27378283]
2. Park, M.R., Chen, X., Lang, D.E., Ng, K.KS. and Facchini, P.J. Heterodimeric O-methyltransferases involved in the biosynthesis of noscapine in opium poppy. Plant J. 95 (2018) 252-267. [PMID: 29723437]
Accepted name: malonyl-S-ACP:biotin-protein carboxyltransferase
Reaction: a malonyl-[acyl-carrier protein] + a biotinyl-[protein] = an acetyl-[acyl-carrier protein] + a carboxybiotinyl-[protein]
For diagram of reaction click here
Other name(s): malonyl-S-acyl-carrier protein:biotin-protein carboxyltransferase; MadC/MadD; MadC,D; malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxyltransferase
Systematic name: malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxytransferase
Comments: Derived from the components MadC and MadD of the anaerobic bacterium Malonomonas rubra, this enzyme is a component of EC 7.2.4.4, biotin-dependent malonate decarboxylase. The carboxy group is transferred from malonate to the prosthetic group of the biotin protein (MadF) with retention of configuration [2]. Similar to EC 4.1.1.87, malonyl-S-ACP decarboxylase, which forms part of the biotin-independent malonate decarboxylase (EC 4.1.1.88), this enzyme also follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetyl-[acyl-carrier protein] [3].
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103-115. [PMID: 9128730]
2. Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153-1154.
3. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
Accepted name: acetyl-S-ACP:malonate ACP transferase
Reaction: an acetyl-[acyl-carrier protein] + malonate = a malonyl-[acyl-carrier protein] + acetate
For diagram of reaction click here
Other name(s): acetyl-S-ACP:malonate ACP-SH transferase; acetyl-S-acyl-carrier protein:malonate acyl-carrier-protein-transferase; MdcA; MadA; ACP transferase; malonate/acetyl-CoA transferase; malonate:ACP transferase; acetyl-S-acyl carrier protein:malonate acyl carrier protein-SH transferase
Systematic name: acetyl-[acyl-carrier-protein]:malonate S-[acyl-carrier-protein]transferase
Comments: This is the first step in the catalysis of malonate decarboxylation and involves the exchange of an acetyl thioester residue bound to the activated acyl-carrier protein (ACP) subunit of the malonate decarboxylase complex for a malonyl thioester residue [2]. This enzyme forms the α subunit of the multienzyme complexes biotin-independent malonate decarboxylase (EC 4.1.1.88) and biotin-dependent malonate decarboxylase (EC 7.2.4.4). The enzyme can also use acetyl-CoA as a substrate but more slowly [4].
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48-56. [PMID: 18251085]
2. Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530-538. [PMID: 9208947]
3. Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683-690. [PMID: 10561613]
4. Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214-217. [PMID: 12619701]
5. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
Accepted name: 2-oxo-3-(phosphooxy)propyl 3-oxoalkanoate synthase
Reaction: a medium-chain 3-oxoacyl-[acyl-carrier protein] + glycerone phosphate = 2-oxo-3-(phosphooxy)propyl 3-oxoalkanoate + a holo-[acyl-carrier protein]
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
Other name(s): afsA (gene name); scbA (gene name); barX (gene name)
Systematic name: 3-oxoacyl-[acyl-carrier protein]:glycerone phosphate 3-oxonacylltransferase
Comments: The enzyme catalyses the first committed step in the biosynthesis of γ-butyrolactone autoregulators that control secondary metabolism and morphological development in Streptomyces bacteria.
References:
1. Horinouchi, S., Suzuki, H., Nishiyama, M. and Beppu, T. Nucleotide sequence and transcriptional analysis of the Streptomyces griseus gene (afsA) responsible for A-factor biosynthesis. J. Bacteriol. 171 (1989) 1206-1210. [PMID: 2492509]
2. Kato, J.Y., Funa, N., Watanabe, H., Ohnishi, Y. and Horinouchi, S. Biosynthesis of γ-butyrolactone autoregulators that switch on secondary metabolism and morphological development in Streptomyces. Proc. Natl Acad. Sci. USA 104 (2007) 2378-2383. [PMID: 17277085]
3. Hsiao, N.H., Soding, J., Linke, D., Lange, C., Hertweck, C., Wohlleben, W. and Takano, E. ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize γ-butyrolactones. Microbiology 153 (2007) 1394-1404. [PMID: 17464053]
4. Lee, Y.J., Kitani, S. and Nihira, T. Null mutation analysis of an afsA-family gene, barX, that is involved in biosynthesis of the γ-butyrolactone autoregulator in Streptomyces virginiae. Microbiology 156 (2010) 206-210. [PMID: 19778967]
Accepted name: mycolipenoyl-CoA—2-(long-chain-fatty acyl)-trehalose mycolipenoyltransferase
Reaction: a mycolipenoyl-CoA + a 2-(long-chain-fatty acyl)-trehalose = a 2-(long-chain fatty acyl)-3-mycolipenoyl-trehalose + CoA
Glossary: a mycolipenoyl-CoA = a (2E,2S,4S,6S)-2,4,6-trimethyl-2-enoyl-CoA
polyacyltrehalose = PAT = a 2-(long-chain fatty acyl)-2',3,4',6-tetramycolipenoyl-trehalose
Other name(s): papA3 (gene name)
Systematic name: mycolipenoyl-CoA:2-(long-chain-fatty acyl)-trehalose 3-mycolipenoyltransferase
Comments: The enzyme, characterized from the bacterium Mycobacterium tuberculosis, participates in the biosynthesis of polyacyltrehalose (PAT), a pentaacylated, trehalose-based glycolipid found in the cell wall of pathogenic strains. The enzyme catalyses two successive activities - it first transfers an acyl (often palmitoyl) group to position 2 (see EC 2.3.1.279, long-chain-acyl-CoA—trehalose acyltransferase), followed by the transfer of a mycolipenyl group to position 3.
References:
1. Hatzios, S.K., Schelle, M.W., Holsclaw, C.M., Behrens, C.R., Botyanszki, Z., Lin, F.L., Carlson, B.L., Kumar, P., Leary, J.A. and Bertozzi, C.R. PapA3 is an acyltransferase required for polyacyltrehalose biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem 284 (2009) 12745-12751. [PMID: 19276083]
Accepted name: long-chain-acyl-CoA—trehalose acyltransferase
Reaction: a long-chain fatty acyl-CoA + α,α-trehalose = a 2-(long-chain-fatty acyl)-trehalose + CoA
Glossary: polyacyltrehalose = PAT = a 2-(long-chain fatty acyl)-2',3,4',6-tetramycolipenoyl-trehalose
a mycolipenoyl-CoA = a (2E,2S,4S,6S)-2,4,6-trimethyl-2-enoyl-CoA
Other name(s): papA3 (gene name)
Systematic name: long-chain fatty acyl-CoA:α,α-trehalose 2-acyltransferase
Comments: The enzyme, characterized from the bacterium Mycobacterium tuberculosis, participates in the biosynthesis of polyacyltrehalose (PAT), a pentaacylated, trehalose-based glycolipid found in the cell wall of pathogenic strains. The enzyme catalyses two successive activities - it first transfers an acyl (often palmitoyl) group to position 2, followed by the transfer of a mycolipenyl group to position 3 (see EC 2.3.1.278, mycolipenoyl-CoA—2-(long-chain-fatty acyl)-trehalose mycolipenoyltransferase).
References:
1. Hatzios, S.K., Schelle, M.W., Holsclaw, C.M., Behrens, C.R., Botyanszki, Z., Lin, F.L., Carlson, B.L., Kumar, P., Leary, J.A. and Bertozzi, C.R. PapA3 is an acyltransferase required for polyacyltrehalose biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem 284 (2009) 12745-12751. [PMID: 19276083]
Accepted name: (aminoalkyl)phosphonate N-acetyltransferase
Reaction: acetyl-CoA + (aminomethyl)phosphonate = CoA + (acetamidomethyl)phosphonate
Other name(s): phnO (gene name)
Systematic name: acetyl-CoA:(aminomethyl)phosphonate N-acetyltransferase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is able to acetylate a range of (aminoalkyl)phosphonic acids. Requires a divalent metal ion for activity.
References:
1. Errey, J.C. and Blanchard, J.S. Functional annotation and kinetic characterization of PhnO from Salmonella enterica. Biochemistry 45 (2006) 3033-3039. [PMID: 16503658]
2. Hove-Jensen, B., McSorley, F.R. and Zechel, D.L. Catabolism and detoxification of 1-aminoalkylphosphonic acids: N-acetylation by the phnO gene product. PLoS One 7 (2012) e46416. [PMID: 23056305]
Accepted name: 2-hydroxyflavanone C-glucosyltransferase
Reaction: UDP-α-D-glucose + a 2'-hydroxy-β-oxodihydrochalcone = UDP + a 3'-(β-D-glucopyranosyl)-2'-hydroxy-β-oxodihydrochalcone
For diagram of reaction click here
Glossary: 2'-hydroxy-β-oxodihydrochalcone = 1-(2-hydroxyphenyl)-3-phenypropan-1,3-dione
3'-(β-D-glucopyranosyl)-2'-hydroxy-β-oxodihydrochalcone = 1-(3-(β-D-glucopyranosyl)-2-hydroxyphenyl)-3-phenylpropan-1,3-dione
Other name(s): OsCGT
Systematic name: UDP-α-D-glucose:2'-hydroxy-β-oxodihydrochalcone C6/8-β-D-glucosyltransferase
Comments: The enzyme has been characterized in Oryza sativa (rice), various Citrus spp., Glycine max (soybean), and Fagopyrum esculentum (buckwheat). Flavanone substrates require a 2-hydroxy group. The meta-stable flavanone substrates such as 2-hydroxynaringenin exist in an equilibrium with open forms such as 1-(4-hydroxyphenyl)-3-(2,4,6-trihydroxyphenyl)propane-1,3-dione, which are the actual substrates for the glucosyl-transfer reaction (see EC 1.14.14.162, flavanone 2-hydroxylase). The enzyme can also act on dihydrochalcones. The enzymes from citrus plants can catalyse a second C-glycosylation reaction at position 5.
References:
1. Brazier-Hicks, M., Evans, K.M., Gershater, M.C., Puschmann, H., Steel, P.G. and Edwards, R. The C-glycosylation of flavonoids in cereals. J. Biol. Chem. 284 (2009) 17926-17934. [PMID: 19411659]
2. Nagatomo, Y., Usui, S., Ito, T., Kato, A., Shimosaka, M. and Taguchi, G. Purification, molecular cloning and functional characterization of flavonoid C-glucosyltransferases from Fagopyrum esculentum M. (buckwheat) cotyledon. Plant J. 80 (2014) 437-448. [PMID: 25142187]
3. Hirade, Y., Kotoku, N., Terasaka, K., Saijo-Hamano, Y., Fukumoto, A. and Mizukami, H. Identification and functional analysis of 2-hydroxyflavanone C-glucosyltransferase in soybean (Glycine max). FEBS Lett. 589 (2015) 1778-1786. [PMID: 25979175]
4. Ito, T., Fujimoto, S., Suito, F., Shimosaka, M. and Taguchi, G. C-Glycosyltransferases catalyzing the formation of di-C-glucosyl flavonoids in citrus plants. Plant J. 91 (2017) 187-198. [PMID: 28370711]
Accepted name: lycopaoctaene synthase
Reaction: 2 geranylgeranyl diphosphate + NADPH + H+ = lycopaoctaene + 2 diphosphate + NADP+ (overall reaction)
(1a) 2 geranylgeranyl diphosphate = diphosphate + prephytoene diphosphate
(1b) prephytoene diphosphate + NADPH + H+ = lycopaoctaene + diphosphate + NADP+
For diagram of reaction click here
Glossary: lycopaoctaene = 15,15'-dihydrophytoene = (6E,10E,14E,18E,22E,26E)-2,6,10,14,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaene
Other name(s): LOS (gene name)
Systematic name: geranylgeranyl diphosphate:geranylgeranyl diphosphate geranylgeranyltransferase
Comments: The enzyme, characterized from the green microalga Botryococcus braunii race L, in involved in biosynthesis of (14E,18E)-lycopadiene. In vitro, the enzyme can accept (2E,6E)-farnesyl diphosphate and phytyl diphosphate as substrates, and is also able to catalyse the condensation of two different substrate molecules, forming chimeric products. However, the use of these alternative substrates is not significant in vivo.
References:
1. Thapa, H.R., Naik, M.T., Okada, S., Takada, K., Molnar, I., Xu, Y. and Devarenne, T.P. A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L. Nat Commun 7 (2016) 11198. [PMID: 27050299]
2. Thapa, H.R., Tang, S., Sacchettini, J.C. and Devarenne, T.P. Tetraterpene synthase substrate and product specificity in the green microalga Botryococcus braunii Race L. ACS Chem. Biol. 12 (2017) 2408-2416. [PMID: 28813599]
Accepted name: lycopene elongase/hydratase (flavuxanthin-forming)
Reaction: (1) dimethylallyl diphosphate + all-trans-lycopene + acceptor + H2O = nonaflavuxanthin + reduced electron acceptor + diphosphate
(2) dimethylallyl diphosphate + nonaflavuxanthin + acceptor + H2O = flavuxanthin + reduced electron acceptor + diphosphate
For diagram of reaction click here
Glossary: flavuxanthin = 2,2'-bis-(4-hydroxy-3-methylbut-2-enyl)-1,16,1',16'-tetradehydro-1,2,1',2'-tetrahydro-ψ,ψ-carotene = (2E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E,28E,34E)-5,32-diisopropenyl-2,8,12,16,21,25,29,35-octamethylhexatriaconta-2,8,10,12,14,16,18,20,22,24,26,28,34-tridecaene-1,36-diol
Other name(s): crtEb (gene name)
Systematic name: dimethylallyl-diphosphate:all-trans-lycopene dimethylallyltransferase (hydrating, flavuxanthin-forming)
Comments: The enzyme, characterized from the bacterium Corynebacterium glutamicum, is bifunctional. It catalyses the elongation of the C40 carotenoid all-trans-lycopene by attaching an isoprene unit at C-2, as well as the hydroxylation of the new isoprene unit. The enzyme acts at both ends of the substrate, forming the C50 carotenoid flavuxanthin via the C45 intermediate nonaflavuxanthin. cf. EC 2.5.1.150, lycopene elongase/hydratase (dihydrobisanhydrobacterioruberin-forming).
References:
1. Krubasik, P., Kobayashi, M. and Sandmann, G. Expression and functional analysis of a gene cluster involved in the synthesis of decaprenoxanthin reveals the mechanisms for C50 carotenoid formation. Eur. J. Biochem. 268 (2001) 3702-3708. [PMID: 11432736]
2. Heider, S.A., Peters-Wendisch, P. and Wendisch, V.F. Carotenoid biosynthesis and overproduction in Corynebacterium glutamicum. BMC Microbiol. 12 (2012) 198. [PMID: 22963379]
Accepted name: lycopene elongase/hydratase (dihydrobisanhydrobacterioruberin-forming)
Reaction: (1) dimethylallyl diphosphate + all-trans-lycopene + H2O = dihydroisopentenyldehydrorhodopin + diphosphate
(2) dimethylallyl diphosphate + isopentenyldehydrorhodopin + H2O = dihydrobisanhydrobacterioruberin + diphosphate
For diagram of reaction click here
Glossary: dihydrobisanhydrobacterioruberin = (2S,2S')-2,2'-bis(3-methylbut-2-en-1-yl)-3,3',4,4'-tetradehydro-1,1',2,2'-tetrahydro-ψ,ψ-carotene-1,1'-diol = (3S,4E,6E,8E,10E,12E,14E,16E,18E,20E,22E,24E,26E,30R)-2,6,10,14,19,23,27,31-octamethyl-3,30-bis(3-methylbut-2-en-1-yl)dotriaconta-4,6,8,10,12,14,16,18,20,22,24,26-dodecaene-2,31-diol
Other name(s): lbtA (gene name); lyeJ (gene name)
Systematic name: dimethylallyl-diphosphate:all-trans-lycopene dimethylallyltransferase (hydrating, dihydrobisanhydrobacterioruberin-forming)
Comments: The enzyme, characterized from the bacterium Dietzia sp. CQ4 and the halophilic archaea Halobacterium salinarum and Haloarcula japonica, is bifunctional. It catalyses the elongation of the C40 carotenoid all-trans-lycopene by attaching an isoprene unit at C-2 as well as the hydroxylation of the previous end of the molecule. The enzyme acts at both ends of the substrate, and combined with the action of EC 1.3.99.37, 1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase, it forms the C50 carotenoid dihydrobisanhydrobacterioruberin. cf. EC 2.5.1.149, lycopene elongase/hydratase (flavuxanthin-forming).
References:
1. Tao, L., Yao, H. and Cheng, Q. Genes from a Dietzia sp. for synthesis of C40 and C50 β-cyclic carotenoids. Gene 386 (2007) 90-97. [PMID: 17008032]
2. Dummer, A.M., Bonsall, J.C., Cihla, J.B., Lawry, S.M., Johnson, G.C. and Peck, R.F. Bacterioopsin-mediated regulation of bacterioruberin biosynthesis in Halobacterium salinarum. J. Bacteriol. 193 (2011) 5658-5667. [PMID: 21840984]
3. Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614-1623. [PMID: 25712483]
Accepted name: alkylcobalamin dealkylase
Reaction: an alkylcobalamin + [alkylcobalamin reductase] + glutathione = cob(I)alamin-[alkylcobalamin reductase] + an S-alkylglutathione
Other name(s): MMACHC (gene name)
Systematic name: alkylcobalamin:glutathione S-alkyltransferase
Comments: This mammalian enzyme, which is cytosolic, can bind internalized alkylcobalamins and process them to cob(I)alamin using the thiolate of glutathione for nucleophilic displacement. The product remains bound to the protein, and, following its oxidation to cob(II)alamin, is transferred by the enzyme, together with its interacting partner MMADHC, directly to downstream enzymes involved in adenosylcobalamin and methylcobalamin. In addition to its dealkylase function, the enzyme also catalyse an entirely different decyanase reaction with cyanocobalamin [cf. EC 1.16.1.6, cyanocobalamin reductase (cyanide-eliminating)].
References:
1. Hannibal, L., Kim, J., Brasch, N.E., Wang, S., Rosenblatt, D.S., Banerjee, R. and Jacobsen, D.W. Processing of alkylcobalamins in mammalian cells: A role for the MMACHC (cblC) gene product. Mol Genet Metab 97 (2009) 260-266. [PMID: 19447654]
2. Kim, J., Hannibal, L., Gherasim, C., Jacobsen, D.W. and Banerjee, R. A human vitamin B12 trafficking protein uses glutathione transferase activity for processing alkylcobalamins. J. Biol. Chem. 284 (2009) 33418-33424. [PMID: 19801555]
3. Koutmos, M., Gherasim, C., Smith, J.L. and Banerjee, R. Structural basis of multifunctionality in a vitamin B12-processing enzyme. J. Biol. Chem. 286 (2011) 29780-29787. [PMID: 21697092]
[EC 3.1.27.1 Transferred entry: ribonuclease T2. Now EC 4.6.1.19, ribonuclease T2, since the primary reaction is that of a lyase(EC 3.1.27.1 created 1972 as EC 3.1.4.23, transferred 1978 to EC 3.1.27.1, modified 1981, deleted 2018)]
[EC 3.1.27.2 Transferred entry: Bacillus subtilis ribonuclease. Now EC 4.6.1.22, Bacillus subtilis ribonuclease, since the reaction catalysed is that of a lyase(EC 3.1.27.2 created 1978, deleted 2018)]
[EC 3.1.27.4 Transferred entry: ribonuclease U2. Now EC 4.6.1.20, ribonuclease U2, since the primary reaction is that of a lyase(EC 3.1.27.4 created 1978, modified 1981, deleted 2018)]
[EC 3.1.27.5 Transferred entry: pancreatic ribonuclease. Now EC 4.6.1.18, pancreatic ribonuclease. This reaction is now known to involve an internal-transfer (lyase) process to produce the cyclic derivative, followed by a reversal of that step with water in the "hydrolytic step"[EC 3.1.27.5 created 1972 as EC 3.1.4.22, transferred 1978 to EC 3.1.27.5, modified 1981, deleted 2018]]
[EC 3.1.27.6 Transferred entry: Enterobacter ribonuclease. Now EC 4.6.1.21, Enterobacter ribonuclease, since the primary reaction is that of a lyase(EC 3.1.27.6 created 1978, modified 1981, deleted 2018)]
[EC 3.6.3.10 Transferred entry: H+/K+-exchanging ATPase. Now EC 7.2.2.19, H+/K+-exchanging ATPase(EC 3.6.3.10 created 1984 as EC 3.6.1.36, transferred 2000 to EC 3.6.3.10, deleted 2018)]
[EC 3.6.3.38 Transferred entry: capsular-polysaccharide-transporting ATPase. Now EC 7.6.2.2, ABC-type capsular-polysaccharide transporter(EC 3.6.3.38 created 2000, deleted 2018)]
[EC 3.6.3.49 Transferred entry: channel-conductance-controlling ATPase. Now EC 5.6.1.6, channel-conductance-controlling ATPase(EC 3.6.3.49 created 2000, deleted 2018)]
[EC 3.6.4.1 Transferred entry: myosin ATPase. Now EC 5.6.1.8, myosin ATPase(EC 3.6.4.1 created 1984 as EC 3.6.1.32, transferred 2000 to EC 3.6.4.1, deleted 2018)]
[EC 3.6.4.2 Transferred entry: dynein ATPase. Now EC 5.6.1.2, dynein ATPase(EC 3.6.4.2 created 1984 as EC 3.6.1.33, transferred 2000 to EC 3.6.4.2, deleted 2018)]
[EC 3.6.4.4 Transferred entry: plus-end-directed kinesin ATPase. Now EC 5.6.1.3, plus-end-directed kinesin ATPase(EC 3.6.4.4 created 2000, deleted 2018)]
[EC 3.6.4.5 Transferred entry: minus-end-directed kinesin ATPase. Now EC 5.6.1.4, minus-end-directed kinesin ATPase(EC 3.6.4.5 created 2000, deleted 2018)]
[EC 3.6.4.8 Transferred entry: proteasome ATPase. Now EC 5.6.1.5, proteasome ATPase(EC 3.6.4.8 created 2000, deleted 2018)]
[EC 3.6.4.9 Transferred entry: chaperonin ATPase. Now EC 5.6.1.7, chaperonin ATPase(EC 3.6.4.9 created 2000, deleted 2018)]
Accepted name: biotin-independent malonate decarboxylase
Reaction: malonate + H+ = acetate + CO2
For diagram of the reaction click here
Other name(s): malonate decarboxylase (without biotin); malonate decarboxylase (ambiguous); MDC
Systematic name: malonate carboxy-lyase (biotin-independent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. This enzyme is a cytosolic protein that is biotin-independent. The other type is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components (cf. EC 7.2.4.4, biotin-dependent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. In both enzymes, this is achieved by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-ACP. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4'-phosphate. The individual enzymes involved in carrying out the reaction of this enzyme complex are EC 2.3.1.187 (acetyl-S-ACP:malonate ACP transferase), EC 2.3.1.39 ([acyl-carrier-protein] S-malonyltransferase) and EC 4.1.1.87 (malonyl-S-ACP decarboxylase). The carboxy group is lost with retention of configuration [6].
Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:
References:
1. Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221-228. [PMID: 8620876]
2. Byun, H.S. and Kim, Y.S. Subunit organization of bacterial malonate decarboxylases: the smallest δ subunit as an acyl-carrier protein. J. Biochem. Mol. Biol. 30 (1997) 132-137.
3. Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530-538. [PMID: 9208947]
4. Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37-43. [PMID: 9851033]
5. Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233-13240. [PMID: 11052676]
6. Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93-96. [PMID: 10496981]
7. Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683-690. [PMID: 10561613]
8. Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443-451. [PMID: 12359084]
9. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
[EC 4.1.1.89 Transferred entry: biotin-dependent malonate decarboxylase. Now EC 7.2.4.4, biotin-dependent malonate decarboxylase(EC 4.1.1.89 created 2008, deleted 2018)]
Accepted name: cis-3-alkyl-4-alkyloxetan-2-one decarboxylase
Reaction: a cis-3-alkyl-4-alkyloxetan-2-one = a cis-alkene + CO2
Other name(s): oleB (gene name)
Systematic name: cis-3-alkyl-4-alkyloxetan-2-one carboxy-lyase (cis-alkene-forming)
Comments: The enzyme, found in certain bacterial species, catalyses the last step in a pathway for the production of olefins.
References:
1. Christenson, J.K., Richman, J.E., Jensen, M.R., Neufeld, J.Y., Wilmot, C.M. and Wackett, L.P. β-Lactone synthetase found in the olefin biosynthesis pathway. Biochemistry 56 (2017) 348-351. [PMID: 28029240]
2. Christenson, J.K., Jensen, M.R., Goblirsch, B.R., Mohamed, F., Zhang, W., Wilmot, C.M. and Wackett, L.P. Active multienzyme assemblies for long-chain olefinic hydrocarbon biosynthesis. J. Bacteriol. 199 (2017) . [PMID: 28223313]
Accepted name: dolabradiene synthase
Reaction: ent-copalyl diphosphate = dolabradiene + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: dolabradiene = (4aS,4bR,7S,8aR,10aS)-7-ethenyl-4b,7,10a-trimethyl-1-methylidene-decahydrophenanthrene
Other name(s): KSL4 (gene name)
Systematic name: ent-copalyl-diphosphate diphosphate-lyase (dolabradiene-forming)
Comments: The enzyme, which has been characterized from maize, is involved in the biosynthesis of dolabralexins (type of antifungal phytoalexins).
References:
1. Mafu, S., Ding, Y., Murphy, K.M., Yaacoobi, O., Addison, J.B., Wang, Q., Shen, Z., Briggs, S.P., Bohlmann, J., Castro-Falcon, G., Hughes, C.C., Betsiashvili, M., Huffaker, A., Schmelz, E.A. and Zerbe, P. Discovery, biosynthesis and stress-related accumulation of dolabradiene-derived defenses in maize. Plant Physiol. 176 (2018) 2677-2690. [PMID: 29475898]
Accepted name: eudesmane-5,11-diol synthase
Reaction: (2E,6E)-farnesyl diphosphate + 2 H2O = 7-epi-ent-eudesmane-5,11-diol + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: 7-epi-ent-eudesmane-5,11-diol = (4S,4aS,6R,8aS)-6-(2-hydroxypropan-2-yl)-4,8a-dimethyldecahydronaphthalen-4a-ol
Other name(s): ZmEDS (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, 7-epi-ent-eudesmane-5,11-diol-forming)
Comments: Isolated from the plant Zea mays (maize). The product is named in the reference using a different numbering scheme for eudesmane.
References:
1. Liang, J., Liu, J., Brown, R., Jia, M., Zhou, K., Peters, R.J. and Wang, Q. Direct production of dihydroxylated sesquiterpenoids by a maize terpene synthase. Plant J. 94 (2018) 847-856. [PMID: 29570233]
Accepted name: α-selinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = α-selinene + diphosphate
For diagram of reaction click here
Glossary: α-selinene = (2R,4aR,8aS)-4,8a-dimethyl-2-(prop-1-en-2-yl)-1,2,3,4,4a,5,6,8a-octahydronaphthalene
β-selinene = (4aR,7R,8aS)-4a-methyl-1-methylidene-7-(prop-1-en-2-yl)decahydronaphthalene
aromadendrene = (1aR,4aR,7R,7aR,7bS)-1,1,7-trimethyl-4-methylidenedecahydro-1H-cyclopropa[e]azulene
Other name(s): LfTPS2 (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, α-selinene-forming)
Comments: The enzyme from the plant Ocimum basilicum (sweet basil) also produces β-selinene while that from Liquidambar formosana (Formosan sweet gum) also produces traces of aromadendrene.
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. Chuang, L., Wen, C.H., Lee, Y.R., Lin, Y.L., Hsu, L.R., Wang, S.Y. and Chu, F.H. Identification, functional characterization, and seasonal expression patterns of five sesquiterpene synthases in Liquidambar formosana. J Nat Prod 81 (2018) 1162-1172. [PMID: 29746128]
Accepted name: (-)-5-epieremophilene synthase
Reaction: (2E,6E)-farnesyl-diphosphate = (-)-5-epieremophilene + diphosphate
For diagram of reaction click here
Glossary: (-)-5-epieremophilene = (3R,4aS,5S)-4a,5-dimethyl-3-(prop-1-en-2-yl)-1,2,3,4,4a,5,6,7-octahydronaphthalene
Other name(s): STPS1 (gene name); STP2 (gene name); STP3 (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (-)-epieremophilene-forming]
Comments: The plant Salvia miltiorrhiza (danshen) produces three different forms of the enzyme, encoded by paralogous genes, that exhibit different spacial expression patterns and respond differently to hormone treatment.
References:
1. Fang, X., Li, C.Y., Yang, Y., Cui, M.Y., Chen, X.Y. and Yang, L. Identification of a novel (-)-5-epieremophilene synthase from Salvia miltiorrhiza via transcriptome mining. Front. Plant Sci. 8 (2017) 627. [PMID: 28487717]
Accepted name: β-pinacene synthase
Reaction: geranylgeranyl diphosphate = β-pinacene + diphosphate
For diagram of reaction click here
Glossary: β-pinacene = 4,8,12-trimethyl-1-(propan-2-yl)cyclotetradeca-1,3,7,11-tetraene
Other name(s): PcS
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclizing, β-pinacene-forming)
Comments: Isolated from the slime mould Dictyostelium discoideum. The 1-proR hydrogen atom of geranylgeranyl diphosphate is lost in the reaction.
References:
1. Rinkel, J., Rabe, P., Chen, X., Kollner, T.G., Chen, F. and Dickschat, J.S. Mechanisms of the diterpene cyclases β-pinacene synthase from Dictyostelium discoideum and hydropyrene synthase from Streptomyces clavuligerus. Chemistry 23 (2017) 10501-10505. [PMID: 28696553]
Accepted name: pancreatic ribonuclease
Reaction: (1) an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA] (overall reaction)
(1a) an [RNA] containing cytidine = an [RNA]-3'-cytidine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(1b) an [RNA]-3'-cytidine-2',3'-cyclophosphate + H2O = an [RNA]-3'-cytidine-3'-phosphate
(2) an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(2a) an [RNA] containing uridine = an [RNA]-3'-uridine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
(1b) an [RNA]-3'-uridine-2',3'-cyclophosphate + H2O = an [RNA]-3'-uridine-3'-phosphate
Other name(s): RNase; RNase I; RNase A; pancreatic RNase; ribonuclease I; endoribonuclease I; ribonucleic phosphatase; alkaline ribonuclease; ribonuclease; gene S glycoproteins; Ceratitis capitata alkaline ribonuclease; SLSG glycoproteins; gene S locus-specific glycoproteins; S-genotype-asssocd. glycoproteins; ribonucleate 3'-pyrimidino-oligonucleotidohydrolase
Systematic name: RNA lyase ([RNA]-3'-cytidine/uridine-3'-phosphate and 5'-hydroxy-ribonucleotide-3'-[RNA] producing)
Comments: Specifically cleaves at the 3'-side of pyrimidine (uracil or cytosine) phosphate bonds in RNA. The reaction takes place in two steps, with the 2',3'-cyclic phosphodiester intermediates released from the enzyme at the completion of the first step. Hydrolysis of these cyclic compounds occurs at a much slower rate through a reversal of the first step, in which the -OH group of water substitutes for the 2'-OH group of the ribose used in the first step, and does not take place until essentially all the susceptible 3',5'-phosphodiester bonds have been cyclised. The enzyme can act as an endo- or exo ribonuclease.
References:
1. Anfinsen, C.B. and White, F.H., Jr. The ribonucleases: occurrence, structure, and properties. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2ndedn, vol.5, Academic Press, New York, 1961, pp. 95-122.
2. Beard, J.R. and Razzell, W.E. Purification of alkaline ribonuclease II from mitochondrial and soluble fractions of liver. J. Biol. Chem. 239 (1964) 4186-4193. [PMID: 14247667]
3. Cannistraro, V.J. and Kennell, D. Purification and characterization of ribonuclease M and mRNA degradation in Escherichia coli. Int. J. Biochem. 181 (1989) 363-370. [PMID: 2653829]
4. Cuchillo, C.M., Pares, X., Guasch, A., Barman, T., Travers, F. and Nogues, M.V. The role of 2',3'-cyclic phosphodiesters in the bovine pancreatic ribonuclease A catalysed cleavage of RNA: intermediates or products. FEBS Lett. 333 (1993) 207-210. [PMID: 7693511]
5. Loverix, S., Laus, G., Martins, J.C., Wyns, L. and Steyaert, J. Reconsidering the energetics of ribonuclease catalysed RNA hydrolysis. Eur. J. Biochem. 257 (1998) 286-290. [PMID: 9799130]
Accepted name: ribonuclease T2
Reaction: RNA + H2O = an [RNA fragment]-3'-nucleoside-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(1a) RNA = an [RNA fragment]-3'-nucleoside-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-nucleoside-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-nucleoside-3'-phosphate
Other name(s): ribonuclease II; base-non-specific ribonuclease; nonbase-specific RNase; RNase (non-base specific); non-base specific ribonuclease; nonspecific RNase; RNase Ms; RNase M; RNase II; Escherichia coli ribonuclease II; ribonucleate nucleotido-2'-transferase (cyclizing); acid ribonuclease; RNAase CL; Escherichia coli ribonuclease I' ribonuclease PP2; ribonuclease N2; ribonuclease M; acid RNase; ribonnuclease (non-base specific); ribonuclease (non-base specific); RNase T2; ribonuclease PP3; ribonucleate 3'-oligonucleotide hydrolase; ribonuclease U4
Systematic name: [RNA] 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- nucleoside-2',3'-cyclophosphate-forming and hydrolysing)
Comments: A widely distributed family of related enzymes found in protozoans, plants, bacteria, animals and viruses that cleave ssRNA 3'-phosphate group with little base specificity. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending with a 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses the cyclic products in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
References:
1. Garcia-Segura, J.M., Orozco, M.M., Fominaya, J.M. and Gavilanes, J.G. Purification, molecular and enzymic characterization of an acid RNase from the insect Ceratitis capitata. Eur. J. Biochem. 158 (1986) 367-372. [PMID: 3732273]
2. Heppel, L.A. Pig liver nuclei ribonuclease. In: Cantoni, G.L. and Davies, D.R. (Eds), Procedures in Nucleic Acid Research, Procedures in Nucleic Acid Research, New York, 1966, pp. 31-36.
3. Reddi, K.K. and Mauser, L.J. Studies on the formation of tobacco mosaic virus ribonucleic acid. VI. Mode of degradation of host ribonucleic acid to ribonucleosides and their conversion to ribonucleoside 5'-phosphates. Proc. Natl. Acad. Sci. USA 53 (1965) 607-613. [PMID: 14338240]
4. Uchida, I. and Egami, F. The specificity of ribonuclease T2. J. Biochem. (Tokyo) 61 (1967) 44-53. [PMID: 6048969]
5. Irie, M. and Ohgi, K. Ribonuclease T2. Methods Enzymol. 341 (2001) 42-55. [PMID: 11582795]
6. Luhtala, N. and Parker, R. T2 Family ribonucleases: ancient enzymes with diverse roles. Trends Biochem. Sci. 35 (2010) 253-259. [PMID: 20189811]
Accepted name: ribonuclease U2
Reaction: [RNA] containing adenosine + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(1a) [RNA] containing adenosine = an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-adenosine -3'-phosphate
2 [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment] (overall reaction)
(2a) [RNA] containing guanosine = an [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]
(2b) an [RNA fragment]-3'-guanosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'- guanosine-3'-phosphate
Other name(s): purine specific endoribonuclease; ribonuclease U3; RNase U3; RNase U2; purine-specific ribonuclease; purine-specific RNase; Pleospora RNase; Trichoderma koningi RNase III; ribonuclease (purine)
Systematic name: [RNA]-purine 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-purine-nucleoside -2',3'-cyclophosphate-forming and hydrolysing)
Comments: The enzyme secreted by the fungus Ustilago sphaerogena cleaves at the 3'-phosphate group of purines, and catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending in Ap or Gp with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
References:
1. Glitz, D.G. and Dekker, C.A. Studies on a ribonuclease from Ustilago sphaerogena. I. Purification and properties of the enzyme. Biochemistry 3 (1964) 1391-1399. [PMID: 14230791]
2. Glitz, D.G. and Dekker, C.A. Studies on a ribonuclease from Ustilago sphaerogena. II. Specificity of the enzyme. Biochemistry 3 (1964) 1399-1406. [PMID: 14230792]
3. Uchida, T. and Egami, F. Microbial ribonucleases with special reference to RNases T1, T 2, N 1, and U2. In: Boyer, P.D. (Ed.), The Enzymes, 3rdedn, vol.4, Academic Press, New York, 1971, pp. 205-250.
4. Martinez-Ruiz, A., Garcia-Ortega, L., Kao, R., Onaderra, M., Mancheno, J.M., Davies, J., Martinez del Pozo, A. and Gavilanes, J.G. Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein. FEMS Microbiol. Lett. 189 (2000) 165-169. [PMID: 10930732]
Accepted name: Enterobacter ribonuclease
Reaction: RNA containing adenosine-cytidine + H2O = an [RNA fragment]-3'-cytidine-3'-phosphate + a 5'-a hydroxy-adenosine -3'-[RNA fragment] (overall reaction)
(1a) RNA containing adenosine-cytidine = an [RNA fragment]-3'-cytidine-2',3'-cyclophosphate + a 5'-a hydroxy-adenosine -3'-[RNA fragment]
(1b) an [RNA fragment]-3'-cytidine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-cytidine-3'-phosphate
Systematic name: [RNA]-adenosine-cytidine 5'-hydroxy-adenosoine ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-cytidine-2',3'-cyclophosphate-forming and hydrolysing)
Comments: Preference for cleavage at Cp-A bonds. Homopolymers of A, U or G are not hydrolysed. CpG bonds are hydrolysed less well and there is no detectable hydrolysis between two purines or two pyrimidines.The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending a with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.
References:
1. Levy, C.C. and Goldman, P. Residue specificity of a ribonuclease which hydrolyzes polycytidylic acid. J. Biol. Chem. 245 (1970) 3257-3262. [PMID: 5432809]
2. Marotta, C.A., Levy, C.C., Weissman, S.M. and Varricchio, F. Preferred sites of digestion of a ribonuclease from Enterobacter sp. in the sequence analysis of Bacillus stearothermophilus 5S ribonucleic acid. Biochemistry 12 (1973) 2901-2904. [PMID: 4719125]
Accepted name: Bacillus subtilis ribonuclease
Reaction: RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
Other name(s): Proteus mirabilis RNase; ribonucleate nucleotido-2'-transferase (cyclizing); bacterial RNA lyase; Bacillus subtilis intracellular ribonuclease
Systematic name: [RNA] 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- nucleoside -2',3'-cyclophosphate-forming)
Comments: This enzyme catalyses endonucleolytic cleavage to 2',3'-cyclic nucleotides. The cyclic products may be hydrolysed to the corresponding 3'-phosphates by 2',3'-cyclic-nucleotide 2'-phosphodiesterase (EC 3.1.4.16). The enzyme from B. subtilis is inhibited by ATP.
References:
1. Nishimura, H. and Maruo, B. Intracellular ribonuclease from Bacillus subtilis. Biochim. Biophys. Acta 40 (1960) 355-357. [PMID: 13854124]
2. Yamasaki, M. and Arima, K. Regulation of intracellular ribonuclease of Bacillus subtilis by ATP and ADP. Biochim. Biophys. Acta 139 (1967) 202-204. [PMID: 4962137]
3. Yamasaki, M. and Arima, K. Intracellular ribonuclease of Bacillus subtilis; specific inhibition by ATP and dATP. Biochem. Biophys. Res. Commun. 37 (1969) 430-436. [PMID: 4981632]
4. Center, M.S. and Behal, F.J. Studies on the ribonuclease activity of Proteus mirabilis. Biochim. Biophys. Acta 151 (1968) 698-699. [PMID: 4296400]
Accepted name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate epimerase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate + H2O = AMP + diphosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate
Other name(s): murL (gene name); UDP-MurNAc-L-Ala-L-Glu epimerase
Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate L-glutamate-epimerase
Comments: The enzyme, characterized from the bacterium Xanthomonas oryzae, catalyses epimerization of the terminal L-glutamate in UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate. The reaction proceeds only in one direction and involves an adenylated intermediate. The combined activity of this enzyme and EC 6.3.2.53, UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase, provides an alternative route for incorporating D-glutamate into peptidoglycan, replacing the more common combination of EC 5.1.1.3, glutamate racemase, and EC 6.3.2.9, UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase.
References:
1. Feng, R., Satoh, Y., Ogasawara, Y., Yoshimura, T. and Dairi, T. A glycopeptidyl-glutamate epimerase for bacterial peptidoglycan biosynthesis. J. Am. Chem. Soc. 139 (2017) 4243-4245. [PMID: 28294606]
Accepted name: dynein ATPase
Reaction: ATP + H2O + a dynein associated with a microtubule at position n = ADP + phosphate + a dynein associated with a microtubule at position n-1 (toward the minus end)
Other name(s): dynein adenosine 5'-triphosphatase
Systematic name: ATP phosphohydrolase (tubulin-translocating)
Comments: A multisubunit protein complex associated with microtubules. Hydrolysis of ATP provides energy for the movement of organelles (endosomes, lysosomes, mitochondria) along microtubules to the centrosome towards the microtubule's minus end. It also functions in the movement of eukaryotic flagella and cilia. It consists of two heavy chains (about 500 kDa), three-four intermediate chains (about 70 kDa) and four light chains (about 50 kDa).
References:
1. Summers, K.E. and Gibbons, I.R. Adenosine triphosphate-induced sliding of tubules in trypsin-treated flagella of sea-urchin sperm. Proc. Natl. Acad. Sci. USA 68 (1971) 3092-3096. [PMID: 5289252]
2. Gibbons, I.R. Dynein ATPases as microtubule motors. J. Biol. Chem. 263 (1988) 15837-15840. [PMID: 2972702]
3. Gee, M. and Vallee, R. The role of the dynein stalk in cytoplasmic and flagellar motility. Eur. Biophys. J. 27 (1998) 466-473. [PMID: 9760728]
Accepted name: plus-end-directed kinesin ATPase
Reaction: ATP + H2O + a kinesin associated with a microtubule at position n = ADP + phosphate a kinesin associated with a microtubule at position n+1 (toward the plus end)
Other name(s): kinesin
Systematic name: kinesin ATP phosphohydrolase (plus-end-directed)
Comments: Kinesins are a family of motor proteins that move unidirectionally along microtubules as they hydrolyse ATP. The enzymes described here move towards the plus end of the microtubule, in contrast to EC 5.6.1.2, dynein ATPase and EC 5.6.1.4, minus-end-directed kinesin ATPase. They are involved in organelle movement in mitosis and meiosis, and also power vesicular trafficking toward the synapse in neurons. The motor domain, which contains the ATP- and microtubule-binding activities, is located at the N-terminus while the C-terminus links to the cargo being transported.
References:
1. Vale, R.D., Reese, T.S. and Sheetz, M.P. Identification of a novel force-generating protein, kinesin, in microtubule-based motility. Cell 42 (1985) 39-50. [PMID: 3926325]
2. Kull, F.J., Sablin, E.P., Lau, R., Fletterick, R.J. and Vale, R.D. Crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Nature 380 (1996) 550-555. [PMID: 8606779]
3. Howard, J. Molecular motors: structural adaptations to cellular functions. Nature 389 (1997) 561-567. [PMID: 9335494]
4. Nakagawa, T., Tanaka, Y., Matsuoka, E., Kondo, S., Okada, Y., Noda, F., Kanai, Y. and Hirokawa, N. Identification and classification of 16 new kinesin superfamily (KIF) proteins in mouse genome. Proc. Natl. Acad. Sci. USA 94 (1997) 9654-9659. [PMID: 9275178]
5. Sindelar, C.V. and Downing, K.H. The beginning of kinesin’s force-generating cycle visualized at 9-Å resolution. J. Cell Biol. 177 (2007) 377-385. [PMID: 17470637]
6. Wang, W., Cao, L., Wang, C., Gigant, B. and Knossow, M. Kinesin, 30 years later: Recent insights from structural studies. Protein Sci. 24 (2015) 1047-1056. [PMID: 25975756]
Accepted name: minus-end-directed kinesin ATPase
Reaction: ATP + H2O + a kinesin associated with a microtubule at position (n) = ADP + phosphate + a kinesin associated with a microtubule at position (n-1; toward the minus end)
Other name(s): non-claret disjunctional; ncd (gene name)
Systematic name: kinesin ATP phosphohydrolase (minus-end-directed)
Comments: Kinesins are a family of motor proteins that move unidirectionally along microtubules as they hydrolyse ATP and are involved in organelle movement. This enzyme is similar to EC 5.6.1.3, plus-end-directed kinesin ATPase, but the organization of the different domains differs, resulting in movement in the opposite direction along the microtubules.
References:
1. McDonald, H.B., Stewart, R.J. and Goldstein, L.S. The kinesin-like ncd protein of Drosophila is a minus end-directed microtubule motor. Cell 63 (1990) 1159-1165. [PMID: 2261638]
2. Chandra, R., Salmon, E.D., Erickson, H.P., Lockhart, A. and Endow, S.A. Structural and functional domains of the Drosophila ncd microtubule motor protein. J. Biol. Chem 268 (1993) 9005-9013. [PMID: 8473343]
3. Lockhart, A. and Cross, R.A. Origins of reversed directionality in the ncd molecular motor. EMBO J. 13 (1994) 751-757. [PMID: 8112290]
4. Henningsen, U. and Schliwa, M. Reversal in the direction of movement of a molecular motor. Nature 389 (1997) 93-96. [PMID: 9288974]
5. Sablin, E.P., CASe, R.B., Dai, S.C., Hart, C.L., Ruby, A., Vale, R.D. and Fletterick, R.J. Direction determination in the minus-end-directed kinesin motor ncd. Nature 395 (1998) 813-816. [PMID: 9796817]
Accepted name: proteasome ATPase
Reaction: ATP + H2O + polypeptide = ADP + phosphate + unfolded polypeptide
Systematic name: ATP phosphohydrolase (polypeptide-degrading)
Comments: Belongs to the AAA-type superfamily and, like EC 5.6.1.4 (minus-end-directed kinesin ATPase), is involved in channel gating and polypeptide unfolding before proteolysis in the proteasome. Six ATPase subunits are present in the regulatory particle (RP) of 26S proteasome.
References:
1. Rivett, A.J., Mason, G.G., Murray, R.Z. and Reidlinger, J. Regulation of proteasome structure and function. Mol. Biol. Rep. 24 (1997) 99-102. [PMID: 9228289]
2. Mason, G.G., Murray, R.Z., Pappin, D. and Rivett, A.J. Phosphorylation of ATPase subunits of the 26S proteasome. FEBS Lett. 430 (1998) 269-274. [PMID: 9688553]
Accepted name: channel-conductance-controlling ATPase
Reaction: ATP + H2O + closed Cl- channel = ADP + phosphate + open Cl- channel
Other name(s): cystic fibrosis transmembrane conductance regulator; CFTR (gene name)
Systematic name: ATP phosphohydrolase (channel-conductance-controlling)
Comments: ABC-type (ATP-binding cassette-type) ATPase, characterized by the presence of two similar ATP-binding domains. The enzyme is found in animals, and in humans its absence brings about cystic fibrosis. Unlike most of the ABC transporters, chloride pumping is not directly coupled to ATP hydrolysis. Instead, the passive flow of anions through the channel is gated by cycles of ATP binding and hydrolysis by the ATP-binding domains. The enzyme is also involved in the functioning of other transmembrane channels.
References:
1. Chen, M. and Zhang, J.T. Membrane insertion, processing, and topology of cystic fibrosis transmembrane conductance regulator (CFTR) in microsomal membranes. Mol. Membr. Biol. 13 (1996) 33-40. [PMID: 9147660]
2. Tusnady, G.E., Bakos, E., Varadi, A. and Sarkadi, B. Membrane topology distinguishes a subfamily of the ATP-binding cassette (ABC) transporters. FEBS Lett. 402 (1997) 1-3. [PMID: 9013845]
3. Sheppard, D.N. and Welsh, M.J. Structure and function of the CFTR chloride channel. Physiol. Rev. 79 (1999) S23-S45. [PMID: 9922375]
4. Hwang, T.C. and Sheppard, D.N. Gating of the CFTR Cl- channel by ATP-driven nucleotide-binding domain dimerisation. J. Physiol. 587 (2009) 2151-2161. [PMID: 19332488]
Accepted name: chaperonin ATPase
Reaction: ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Other name(s): chaperonin
Systematic name: ATP phosphohydrolase (polypeptide-unfolding)
Comments: Multisubunit proteins with 2x7 (Type I, in most cells) or 2x8 (Type II, in Archaea) ATP-binding sites involved in maintaining an unfolded polypeptide structure before folding or entry into mitochondria and chloroplasts. Molecular masses of subunits ranges from 10-90 kDa. They are a subclass of molecular chaperones that are related to EC 5.6.1.5 (proteasome ATPase).
References:
1. Hemmingsen, S.M., Woolford, C., van der Vies, S.M., Tilly, K., Dennis, D.T., Georgopoulos, G.C., Hendrix, R.W. and Ellis, R.J. Homologous plant and bacterial proteins: chaperone oligomeric protein assembly. Nature 333 (1988) 330-334. [PMID: 2897629]
2. Lubber, T.H., Donaldson, G.K., Viitanen, P.V. and Gatenby, A.A. Several proteins imported into chloroplasts form stable complexes with the GroEL-related chloroplast molecular chaperone. Plant Cell 1 (1989) 1223-1230. [PMID: 2577724]
3. Ellis, R.J. (Ed.), The Chaperonins, Academic Press, San Diego, 1996.
4. Ranson, N.A., White, H.E. and Saibil, H.R. Chaperonins. Biochem. J. 333 (1998) 233-242. [PMID: 9657960]
Accepted name: myosin ATPase
Reaction: ATP + H2O + myosin bound to actin filament at position n = ADP + phosphate + myosin bound to actin filament at position n+1
Systematic name: ATP phosphohydrolase (actin-translocating)
Comments: Proteins of the contractile apparatus of muscle and nonmuscle cells; myosin molecule consists of two heavy chains (about 200 kDa) and two pairs of light chains (15-27 kDa). The head region of the heavy chain contains actin- and ATP-binding sites. ATP hydrolysis provides energy for actomyosin contraction.
References:
1. Rayment, I. The structural basis of myosin ATPase activity. J. Biol. Chem. 271 (1996) 15850-15853. [PMID: 8663496]
2. Hasson, T. and Mooseker, M.S. Vertebrate unconventional myosins. J. Biol. Chem. 271 (1996) 16431-16434. [PMID: 8690736]
3. Murphy, C.T. and Spudich, J.A. The sequence of the myosin 50-20K loop affects myosin's affinity for actin throughout the actin-myosin ATPase cycle and its maximum ATPase activity. Biochemistry 38 (1999) 3785-3792. [PMID: 10090768]
EC 5.6.2. enzymes altering nucleic acid conformation
EC 5.6.2.1
Accepted name: DNA topoisomerase
Reaction: ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Other name(s): type I DNA topoisomerase; untwisting enzyme; relaxing enzyme; nicking-closing enzyme; swivelase; ω-protein; deoxyribonucleate topoisomerase; topoisomerase
Systematic name: DNA topoisomerase
Comments: These enzymes bring about the conversion of one topological isomer of DNA into another, e.g., the relaxation of superhelical turns in DNA, the interconversion of simple and knotted rings of single-stranded DNA, and the intertwisting of single-stranded rings of complementary sequences, cf. EC 5.6.2.2 DNA topoisomerase (ATP-hydrolysing).
References:
1. Gellert, M. DNA topoisomerases. Annu. Rev. Biochem. 50 (1981) 879-910. [PMID: 6267993]
Accepted name: DNA topoisomerase (ATP-hydrolysing)
Reaction: ATP-dependent breakage, passage and rejoining of double-stranded DNA
Other name(s): type II DNA topoisomerase; DNA-gyrase; deoxyribonucleate topoisomerase; deoxyribonucleic topoisomerase; topoisomerase; DNA topoisomerase II
Systematic name: DNA topoisomerase (ATP-hydrolysing)
Comments: The enzyme can introduce negative superhelical turns into double-stranded circular DNA. One unit has nicking-closing activity, and another catalyses super-twisting and hydrolysis of ATP (cf. EC 5.6.2.1 DNA topoisomerase).
References:
1. Gellert, M. DNA topoisomerases. Annu. Rev. Biochem. 50 (1981) 879-910. [PMID: 6267993]
[EC 5.99.1.2 Transferred entry: DNA topoisomerase. Now EC 5.6.2.1, DNA topoisomerase(EC 5.99.1.2 created 1984, deleted 2018)]
[EC 5.99.1.3 Transferred entry: DNA topoisomerase (ATP-hydrolysing). Now EC 5.6.2.2, DNA topoisomerase (ATP-hydrolysing)(EC 5.99.1.3 created 1984, deleted 2018)]
Accepted name: acetate—[acyl-carrier protein] ligase
Reaction: ATP + acetate + an [acyl-carrier protein] = AMP + diphosphate + an acetyl-[acyl-carrier protein]
For diagram of reaction click here
Other name(s): HS-acyl-carrier protein:acetate ligase; [acyl-carrier protein]:acetate ligase; MadH; ACP-SH:acetate ligase
Systematic name: acetate:[acyl-carrier-protein] ligase (AMP-forming)
Comments: This enzyme, from the anaerobic bacterium Malonomonas rubra, is a component of the multienzyme complex EC 7.2.4.4, biotin-dependent malonate decarboxylase. The enzyme uses the energy from hydrolysis of ATP to convert the thiol group of the acyl-carrier-protein-bound 2'-(5-phosphoribosyl)-3'-dephospho-CoA prosthetic group into its acetyl thioester [2].
Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number:
References:
1. Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117-123. [PMID: 1628643]
2. Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2'-(5"-phosphoribosyl)-3'-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689-4696. [PMID: 8664258]
3. Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103-115. [PMID: 9128730]
4. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
Accepted name: UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanine + L-glutamate = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate
Other name(s): murD2 (gene name); UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate synthetase; UDP-MurNAc-L-Ala-L-Glu synthetase
Systematic name: UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase (ADP-forming)
Comments: The enzyme, characterized from the bacterium Xanthomonas oryzae, catalyses the ligation of a terminal L-glutamate to UDP-N-acetyl-α-D-muramoyl-L-alanine. The combined activity of this enzyme and EC 5.1.1.23, UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate epimerase, provides an alternative route for incorporating D-glutamate into peptidoglycan, replacing the more common combination of EC 5.1.1.3, glutamate racemase, and EC 6.3.2.9, UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase.
References:
1. Feng, R., Satoh, Y., Ogasawara, Y., Yoshimura, T. and Dairi, T. A glycopeptidyl-glutamate epimerase for bacterial peptidoglycan biosynthesis. J. Am. Chem. Soc. 139 (2017) 4243-4245. [PMID: 28294606]
Accepted name: H+/K+-exchanging ATPase
Reaction: ATP + H2O + H+[side 1] + K+[side 2] = ADP + phosphate + H+[side 2] + K+[side 1]
Other name(s): H+-K+-ATPase; H,K-ATPase; (K+ + H+)-ATPase
Systematic name: ATP phosphohydrolase (P-type,H+/K+-exchanging)
Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. A gastric mucosal enzyme that catalyses the efflux of one H+ and the influx of one K+ per ATP hydrolysed.
References:
1. Sachs, G., Collier, R.H., Shoemaker, R.L. and Hirschowitz, B.I. The energy source for gastric H+ secretion. Biochim. Biophys. Acta 162 (1968) 210-219. [PMID: 5682852]
2. Hersey, S.J., Perez, A. Matheravidathu, S. and Sachs, G. Gastric H+-K+-ATPase in situ: evidence for compartmentalization. Am. J. Physiol. 257 (1989) G539-G547. [PMID: 2552824]
3. Rabon, E.C. and Reuben, M.A. The mechanism and structure of the gastric H,K-ATPase. Annu. Rev. Physiol. 52 (1990) 321-344. [PMID: 2158765]
Accepted name: biotin-dependent malonate decarboxylase
Reaction: malonate + H+ + Na+ [side 1] = acetate + CO2 + Na+ [side 2]
For diagram of the reaction click here
Other name(s): malonate decarboxylase (with biotin); malonate decarboxylase (ambiguous)
Systematic name: malonate carboxy-lyase (biotin-dependent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. The enzyme described here is a membrane-bound biotin-dependent, Na+-translocating enzyme [6]. The other type is a biotin-independent cytosolic protein (cf. EC 4.1.1.88, biotin-independent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. Both enzymes achieve this by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-bound form of the enzyme. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4'-phosphate. In the anaerobic bacterium Malonomonas rubra, the components of the multienzyme complex/enzymes involved in carrying out the reactions of this enzyme are as follows: MadA (EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase), MadB (EC 7.2.4.1, carboxybiotin decarboxylase), MadC/MadD (EC 2.1.3.10, malonyl-S-ACP:biotin-protein carboxyltransferase) and MadH (EC 6.2.1.35, acetate--[acyl-carrier protein] ligase). Two other components that are involved are MadE, the acyl-carrier protein and MadF, the biotin protein. The carboxy group is lost with retention of configuration [5].
References:
1. Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117-123. [PMID: 1628643]
2. Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48-56. [PMID: 18251085]
3. Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2'-(5"-phosphoribosyl)-3'-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689-4696. [PMID: 8664258]
4. Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103-115. [PMID: 9128730]
5. Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153-1154.
6. Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443-451. [PMID: 12359084]
7. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
Accepted name: ABC-type capsular-polysaccharide transporter
Reaction: ATP + H2O + capsular polysaccharide-[capsular polysaccharide-binding protein][side 1] = ADP + phosphate + capsular polysaccharide[side 2] + [capsular polysaccharide-binding protein][side 1]
Other name(s): capsular-polysaccharide-transporting ATPase
Systematic name: ATP phosphohydrolase (ABC-type, capsular-polysaccharide-exporting)
Comments: ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains. Does not undergo phosphorylation during the transport process. An enzyme that exports capsular polysaccharide in Gram-negative bacteria.
References:
1. Fath, M.J. and Kolter, R. ABC transporters: bacterial exporters. Microbiol. Rev. 57 (1993) 995-1017. [PMID: 8302219]
2. Paulsen, I.T., Beness, A.M. and Saier, M.H., Jr. Computer-based analysis of the protein constituents of transport systems catalysing export of complex carbohydrates in bacteria. Microbiology 143 (1997) 2685-2699. [PMID: 9274022]
3. Pigeon, R.P. and Silver, R.P. Analysis of the G93E mutant allele of KpsM, the membrane component of an ABC transporter involved in polysialic acid translocation in Escherichia coli K1. FEMS Microbiol. Lett. 156 (1997) 217-222. [PMID: 9513268]
4. Saier, M.H., Jr. Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya. Adv. Microb. Physiol. 40 (1998) 81-136. [PMID: 9889977]
5. Griffiths, J.K. and Sansom, C.E. The Transporter Factsbook, Academic Press, San Diego, 1998.