An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: quinate/shikimate dehydrogenase (NAD+)
Reaction: L-quinate + NAD+ = 3-dehydroquinate + NADH + H+
For diagram of rection, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram. The use of the term '5-dehydroquinate' for this compound is based on an earlier system of numbering.
Other name(s): quinate dehydrogenase (ambiguous); quinic dehydrogenase (ambiguous); quinate:NAD oxidoreductase; quinate 5-dehydrogenase (ambiguous); quinate:NAD+ 5-oxidoreductase
Systematic name: L-quinate:NAD+ 3-oxidoreductase
Comments: The enzyme, found mostly in bacteria (mostly, but not exclusively in Gram-positive bacteria), fungi, and plants, participates in the degradation of quinate and shikimate with a strong preference for NAD+ as a cofactor. While the enzyme can act on both quinate and shikimate, activity is higher with the former. cf. EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), EC 1.1.1.282, quinate/shikimate dehydrogenase [NAD(P)+], and EC 1.1.1.25, shikimate dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9028-28-8
References:
1. Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XIII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase. Biochim. Biophys. Acta 15 (1954) 268-280. [PMID: 13208693]
2. Gamborg, O.L. Aromatic metabolism in plants. III. Quinate dehydrogenase from mung bean cell suspension cultures. Biochim. Biophys. Acta 128 (1966) 483-491.
3. Hawkins, A.R., Giles, N.H. and Kinghorn, J.R. Genetical and biochemical aspects of quinate breakdown in the filamentous fungus Aspergillus nidulans. Biochem. Genet. 20 (1982) 271-286. [PMID: 7049157]
4. Singh, S., Stavrinides, J., Christendat, D. and Guttman, D.S. A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass. Mol. Biol. Evol. 25 (2008) 2221-2232. [PMID: 18669580]
5. Teramoto, H., Inui, M. and Yukawa, H. Regulation of expression of genes involved in quinate and shikimate utilization in Corynebacterium glutamicum. Appl. Environ. Microbiol. 75 (2009) 3461-3468. [PMID: 19376919]
6. Kubota, T., Tanaka, Y., Hiraga, K., Inui, M. and Yukawa, H. Characterization of shikimate dehydrogenase homologues of Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 97 (2013) 8139-8149. [PMID: 23306642]
7. Peek, J. and Christendat, D. The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework. Arch. Biochem. Biophys. 566 (2015) 85-99. [PMID: 25524738]
Accepted name: shikimate dehydrogenase (NADP+)
Reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+
For diagram of reaction, click here
Other name(s): shikimate dehydrogenase; dehydroshikimic reductase; shikimate oxidoreductase; shikimate:NADP+ oxidoreductase; 5-dehydroshikimate reductase; shikimate 5-dehydrogenase; 5-dehydroshikimic reductase; DHS reductase; shikimate:NADP+ 5-oxidoreductase; AroE
Systematic name: shikimate:NADP+ 3-oxidoreductase
Comments: NAD+ cannot replace NADP+ [3]. In higher organisms, this enzyme forms part of a multienzyme complex with EC 4.2.1.10, 3-dehydroquinate dehydratase [4]. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.282, quinate/shikimate dehydrogenase [NAD(P)+].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-87-3
References:
1. Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XIII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase. Biochim. Biophys. Acta 15 (1954) 268-280. [PMID: 13208693]
2. Yaniv, H. and Gilvarg, C. Aromatic biosynthesis. XIV. 5-Dehydroshikimic reductase. J. Biol. Chem. 213 (1955) 787-795. [PMID: 14367339]
3. Balinsky, D. and Davies, D.D. Aromatic biosynthesis in higher plants. 1. Preparation and properties of dehydroshikimic reductase. Biochem. J. 80 (1961) 292-296. [PMID: 13686342]
4. Chaudhuri, S. and Coggins, J.R. The purification of shikimate dehydrogenase from Escherichia coli. Biochem. J. 226 (1985) 217-223. [PMID: 3883995]
5. Anton, I.A. and Coggins, J.R. Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase. Biochem. J. 249 (1988) 319-326. [PMID: 3277621]
6. Ye, S., Von Delft, F., Brooun, A., Knuth, M.W., Swanson, R.V. and McRee, D.E. The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode. J. Bacteriol. 185 (2003) 4144-4151. [PMID: 12837789]
Accepted name: quinate/shikimate dehydrogenase [NAD(P)+]
Reaction: (1) L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H + H+
(2) shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H + H+
For diagram of reaction, click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram. The use of the term '5-dehydroquinate' for this compound is based on an earlier system of numbering.
Other name(s): YdiB; quinate/shikimate dehydrogenase (ambiguous)
Systematic name: L-quinate:NAD(P)+ 3-oxidoreductase
Comments: This is the second shikimate dehydrogenase enzyme found in Escherichia coli. It can use both quinate and shikimate as substrates and either NAD+ or NADP+ as acceptor. The low catalytic efficiency with both quinate and shikimate suggests that neither may be the physiological substrate. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.25, shikimate dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Michel, G., Roszak, A.W., Sauvé, V., Maclean, J., Matte, A., Coggins, J.R., Cygler, M. and Lapthorn, A.J. Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activities. J. Biol. Chem. 278 (2003) 19463-19472. [PMID: 12637497]
2. Benach, J., Lee, I., Edstrom, W., Kuzin, A.P., Chiang, Y., Acton, T.B., Montelione, G.T. and Hunt, J.F. The 2.3-Å crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J. Biol. Chem. 278 (2003) 19176-19182. [PMID: 12624088]
Accepted name: levoglucosan dehydrogenase
Reaction: levoglucosan + NAD+ = 3-dehydrolevoglucosan + NADH + H+
Glossary: levoglucosan = 1,6-anhydro-β-D-glucopyranose
Other name(s): 1,6-anhydro-β-D-glucose dehydrogenase
Systematic name: 1,6-anhydro-β-D-glucopyranose:NAD+ 3-oxidoreductase
Comments: Levoglucosan is formed from the pyrolysis of carbohydrates such as starch and cellulose and is an important molecular marker for pollution from biomass burning. This enzyme is present only in bacteria, and has been characterized from Arthrobacter sp. I-552 and Pseudarthrobacter phenanthrenivorans. cf. EC 2.7.1.232, levoglucosan kinase.
References:
1. Nakahara, K., Kitamura, Y., Yamagishi, Y., Shoun, H. and Yasui, T. Levoglucosan dehydrogenase involved in the assimilation of levoglucosan in Arthrobacter sp. I-552. Biosci. Biotechnol. Biochem. 58 (1994) 2193-2196. [PMID: 7765713]
2. Sugiura, M., Nakahara, M., Yamada, C., Arakawa, T., Kitaoka, M. and Fushinobu, S. Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase. J. Biol. Chem. 293 (2018) 17375-17386. [PMID: 30224354]
Accepted name: quinate/shikimate dehydrogenase (quinone)
Reaction: quinate + quinone = 3-dehydroquinate + quinol
For diagram of reaction click here
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram. The use of the term '5-dehydroquinate' for this compound is based on an earlier system of numbering.
Other name(s): NAD(P)+-independent quinate dehydrogenase; quinate:pyrroloquinoline-quinone 5-oxidoreductase; quinate dehydrogenase (quinone)
Systematic name: quinate:quinol 3-oxidoreductase
Comments: The enzyme is membrane-bound. Does not use NAD(P)+ as acceptor. Contains pyrroloquinoline-quinone. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.1.282, quinate/shikimate dehydrogenase [NAD(P)+], and EC 1.1.1.25, shikimate dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 115299-99-5
References:
1. van Kleef, M.A.G. and Duine, J.A. Bacterial NAD(P)-independent quinate dehydrogenase is a quinoprotein. Arch. Microbiol. 150 (1988) 32-36. [PMID: 3044290]
2. Adachi, O., Tanasupawat, S., Yoshihara, N., Toyama, H. and Matsushita, K. 3-Dehydroquinate production by oxidative fermentation and further conversion of 3-dehydroquinate to the intermediates in the shikimate pathway. Biosci. Biotechnol. Biochem. 67 (2003) 2124-2131. [PMID: 14586099]
3. Vangnai, A.S., Toyama, H., De-Eknamkul, W., Yoshihara, N., Adachi, O. and Matsushita, K. Quinate oxidation in Gluconobacter oxydans IFO3244: purification and characterization of quinoprotein quinate dehydrogenase. FEMS Microbiol. Lett. 241 (2004) 157-162. [PMID: 15598527]
Accepted name: [amino-group carrier protein]-5-phospho-L-glutamate reductase
Reaction: an [amino-group carrier protein]-C-terminal-γ-(L-glutamate 5-semialdehyde-2-yl)-L-glutamate + phosphate + NADP+ = an [amino-group carrier protein]-C-terminal-γ-(5-phospho-L-glutamyl)-L-glutamate + NADPH + H+
Other name(s): lysY (gene name)
Systematic name: [amino-group carrier protein]-C-terminal-γ-(L-glutamate 5-semialdehyde-2-yl)-L-glutamate:NADP+ 5-oxidoreductase (phosphorylating)
Comments: The enzyme participates in an L-arginine biosynthesis pathway in certain species of archaea and bacteria. In some organisms the enzyme is bifunctional and also catalyses the activity of EC 1.2.1.103, [amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase.
References:
1. Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277-283. [PMID: 23434852]
2. Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630-21643. [PMID: 27566549]
Accepted name: butanoyl-CoA dehydrogenase complex (NAD+, ferredoxin)
Reaction: butanoyl-CoA + 2 NAD+ + 2 reduced ferredoxin [iron-sulfur] cluster = (E)-but-2-enoyl-CoA + 2 NADH + 2 oxidized ferredoxin [iron-sulfur] cluster
Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA
Other name(s): bifurcating butyryl-CoA dehydrogenase; butyryl-CoA dehydrogenase/Etf complex; Etf-Bcd complex; bifurcating butanoyl-CoA dehydrogenase; butanoyl-CoA dehydrogenase/Etf complex; butanoyl-CoA dehydrogenase (NAD+, ferredoxin)
Systematic name: butanoyl-CoA:NAD+, ferredoxin oxidoreductase
Comments: The enzyme is a complex of a flavin-containing dehydrogenase component (Bcd) and an electron-transfer flavoprotein dimer (EtfAB). The enzyme complex, isolated from the bacteria Acidaminococcus fermentans and butanoate-producing Clostridia species, couples the exergonic reduction of (E)-but-2-enoyl-CoA to butanoyl-CoA by NADH to the endergonic reduction of ferredoxin by NADH, using electron bifurcation to overcome the steep energy barrier in ferredoxin reduction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Li, F., Hinderberger, J., Seedorf, H., Zhang, J., Buckel, W. and Thauer, R.K. Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J. Bacteriol. 190 (2008) 843-850. [PMID: 17993531]
2. Aboulnaga el,-H., Pinkenburg, O., Schiffels, J., El-Refai, A., Buckel, W. and Selmer, T. Effect of an oxygen-tolerant bifurcating butyryl coenzyme A dehydrogenase/electron-transferring flavoprotein complex from Clostridium difficile on butyrate production in Escherichia coli. J. Bacteriol. 195 (2013) 3704-3713. [PMID: 23772070]
3. Chowdhury, N.P., Mowafy, A.M., Demmer, J.K., Upadhyay, V., Koelzer, S., Jayamani, E., Kahnt, J., Hornung, M., Demmer, U., Ermler, U. and Buckel, W. Studies on the mechanism of electron bifurcation catalyzed by electron transferring flavoprotein (Etf) and butyryl-CoA dehydrogenase (Bcd) of Acidaminococcus fermentans. J. Biol. Chem. 289 (2014) 5145-5157. [PMID: 24379410]
4. Chowdhury, N.P., Kahnt, J. and Buckel, W. Reduction of ferredoxin or oxygen by flavin-based electron bifurcation in Megasphaera elsdenii. FEBS J. 282 (2015) 3149-3160. [PMID: 25903584]
Accepted name: dehydro coenzyme F420 reductase
Reaction: oxidized coenzyme F420-0 + FMN = dehydro coenzyme F420-0 + FMNH2
Glossary: dehydro coenzyme F420-0 = 2-{[5-deoxy-5-(8-hydroxy-2,4-dioxopyrimidino[4,5-b]quinolin-10(2H)-yl)-L-ribityloxy]hydroxyphosphoryloxy}prop-2-enoate
Other name(s): fbiB (gene name)
Comments: This enzyme is involved in the biosynthesis of coenzyme F420, a redox-active cofactor found in all methanogenic archaea, as well as some eubacteria. In some eubacteria the enzyme is multifunctional, also catalysing the activities of EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase, and EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase.
References:
1. Bashiri, G., Antoney, J., Jirgis, E.NM., Shah, M.V., Ney, B., Copp, J., Stuteley, S.M., Sreebhavan, S., Palmer, B., Middleditch, M., Tokuriki, N., Greening, C., Scott, C., Baker, E.N. and Jackson, C.J. A revised biosynthetic pathway for the cofactor F420 in prokaryotes. Nat. Commun. 10 (2019) 1558. [PMID: 30952857]
Accepted name: [mycofactocin precursor peptide]-tyrosine decarboxylase
Reaction: C-terminal [mycofactocin precursor peptide]-glycyl-L-valyl-L-tyrosine + S-adenosyl-L-methionine = C-terminal [mycofactocin precursor peptide]-glycyl-L-valyl-4-[2-aminoethenyl]phenol + CO2 + 5'-deoxyadenosine + L-methionine
Other name(s): mftC (gene name)
Systematic name: C-terminal [mycofactocin precursor peptide]-glycyl-L-valyl-L-tyrosine L-tyrosine-carboxylyase
Comments: This is a bifunctional radical AdoMet (radical SAM) enzyme that catalyses the first two steps in the biosynthesis of the enzyme cofactor mycofactocin. Activity requires the presence of the MftB chaperone. The other activity of the enzyme is EC 4.1.99.26, 3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethylpyrrolidin-2-one synthase.
References:
1. Haft, D.H. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. BMC Genomics 12 (2011) 21. [PMID: 21223593]
2. Bruender, N.A. and Bandarian, V. The radical S-adenosyl-L-methionine enzyme MftC catalyzes an oxidative decarboxylation of the C-terminus of the MftA peptide. Biochemistry 55 (2016) 2813-2816. [PMID: 27158836]
3. Khaliullin, B., Ayikpoe, R., Tuttle, M. and Latham, J.A. Mechanistic elucidation of the mycofactocin-biosynthetic radical S-adenosylmethionine protein, MftC. J. Biol. Chem. 292 (2017) 13022-13033. [PMID: 28634235]
4. Ayikpoe, R., Ngendahimana, T., Langton, M., Bonitatibus, S., Walker, L.M., Eaton, S.S., Eaton, G.R., Pandelia, M.E., Elliott, S.J. and Latham, J.A. Spectroscopic and electrochemical characterization of the mycofactocin biosynthetic protein, MftC, provides insight into its redox flipping mechanism. Biochemistry 58 (2019) 940-950. [PMID: 30628436]
Accepted name: methylenetetrahydrofolate reductase [NAD(P)H]
Reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+
For diagram of reaction, click here and for diagram of C1 metabolism, click here
Other name(s): MTHFR (gene name)
Systematic name: 5-methyltetrahydrofolate:NAD(P)+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme catalyses the reversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, playing an important role in folate metabolism by regulating the distribution of one-carbon moieties between cellular methylation reactions and nucleic acid synthesis. This enzyme, characterized from Protozoan parasites of the genus Leishmania, is unique among similar characterized eukaryotic enzymes in that it lacks the C-terminal allosteric regulatory domain (allowing it to catalyse a reversible reaction) and uses NADH and NADPH with equal efficiency under physiological conditions. cf. EC 1.5.1.53, methylenetetrahydrofolate reductase (NADPH); EC 1.5.1.54, methylenetetrahydrofolate reductase (NADH); and EC 1.5.7.1, methylenetetrahydrofolate reductase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 71822-25-8
References:
1. Vickers, T.J., Orsomando, G., de la Garza, R.D., Scott, D.A., Kang, S.O., Hanson, A.D. and Beverley, S.M. Biochemical and genetic analysis of methylenetetrahydrofolate reductase in Leishmania metabolism and virulence. J. Biol. Chem. 281 (2006) 38150-38158. [PMID: 17032644]
Accepted name: methylenetetrahydrofolate reductase (NADPH)
Reaction: 5-methyltetrahydrofolate + NADP+ = 5,10-methylenetetrahydrofolate + NADPH + H+
For diagram of reaction, click here and for its place in C1 metabolism, click here
Other name(s): MTHFR (gene name); methylenetetrahydrofolate (reduced nicotinamide adenine dinucleotide phosphate) reductase; 5,10-methylenetetrahydrofolate reductase (NADPH); 5,10-methylenetetrahydrofolic acid reductase (ambiguous); 5,10-CH2-H4folate reductase (ambiguous); methylenetetrahydrofolate reductase (NADPH2); 5,10-methylenetetrahydrofolate reductase (ambiguous); methylenetetrahydrofolate reductase (ambiguous); N5,10-methylenetetrahydrofolate reductase (ambiguous); 5,10-methylenetetrahydropteroylglutamate reductase (ambiguous); N5,N10-methylenetetrahydrofolate reductase (ambiguous); methylenetetrahydrofolic acid reductase (ambiguous); 5-methyltetrahydrofolate:(acceptor) oxidoreductase (incorrect); 5,10-methylenetetrahydrofolate reductase (FADH2) (ambiguous)
Systematic name: 5-methyltetrahydrofolate:NADP+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme from yeast and mammals catalyses a physiologically irreversible reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using NADPH as the electron donor. It plays an important role in folate metabolism by regulating the distribution of one-carbon moieties between cellular methylation reactions and nucleic acid synthesis. The enzyme contains an N-terminal catalytic domain and a C-terminal allosteric regulatory domain that binds S-adenosyl-L-methionine, which acts as an inhibitor. cf. EC 1.5.1.54, methylenetetrahydrofolate reductase (NADH); EC 1.5.1.20, methylenetetrahydrofolate reductase [NAD(P)H]; and EC 1.5.7.1, methylenetetrahydrofolate reductase (ferredoxin).
References:
1. Donaldson, K.O. and Keresztesy, J.C. Naturally occurring forms of folic acid. I. J. Biol. Chem. 234 (1959) 3235-3240. [PMID: 13817476]
2. Kutzbach, C. and Stokstad, E.L.R. Mammalian methylenetetrahydrofolate reductase. Partial purification, properties, and inhibition by S-adenosylmethionine. Biochim. Biophys. Acta 250 (1971) 459-477. [PMID: 4399897]
3. Daubner, S.C. and Matthews, R.T. Purification and properties of methylenetetrahydrofolate reductase from pig liver. J. Biol. Chem. 257 (1982) 140-145. [PMID: 6975779]
4. Zhou, J., Kang, S.S., Wong, P.W., Fournier, B. and Rozen, R. Purification and characterization of methylenetetrahydrofolate reductase from human cadaver liver. Biochem Med Metab Biol 43 (1990) 234-242. [PMID: 2383427]
5. Roje, S., Chan, S.Y., Kaplan, F., Raymond, R.K., Horne, D.W., Appling, D.R. and Hanson, A.D. Metabolic engineering in yeast demonstrates that S-adenosylmethionine controls flux through the methylenetetrahydrofolate reductase reaction in vivo. J. Biol. Chem. 277 (2002) 4056-4061. [PMID: 11729203]
6. Froese, D.S., Kopec, J., Rembeza, E., Bezerra, G.A., Oberholzer, A.E., Suormala, T., Lutz, S., Chalk, R., Borkowska, O., Baumgartner, M.R. and Yue, W.W. Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nat. Commun. 9 (2018) 2261. [PMID: 29891918]
Accepted name: methylenetetrahydrofolate reductase (NADH)
Reaction: 5-methyltetrahydrofolate + NAD+ = 5,10-methylenetetrahydrofolate + NADH + H+
For diagram of reaction, click here and for its place in C1 metabolism, click here
Other name(s): metF (gene name); 5,10-methylenetetrahydrofolic acid reductase (ambiguous); 5,10-CH2-H4folate reductase (ambiguous); methylenetetrahydrofolate (reduced riboflavin adenine dinucleotide) reductase; 5,10-methylenetetrahydrofolate reductase (ambiguous); methylenetetrahydrofolate reductase (ambiguous); N5,10-methylenetetrahydrofolate reductase (ambiguous); 5,10-methylenetetrahydropteroylglutamate reductase (ambiguous); N5,N10-methylenetetrahydrofolate reductase (ambiguous); methylenetetrahydrofolic acid reductase (ambiguous); 5-methyltetrahydrofolate:(acceptor) oxidoreductase (incorrect); 5,10-methylenetetrahydrofolate reductase (FADH2) (ambiguous)
Systematic name: 5-methyltetrahydrofolate:NAD+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme, found in plants and some bacteria, catalyses the reversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using NADH as the electron donor. It play an important role in folate metabolism by regulating the distribution of one-carbon moieties between cellular methylation reactions and nucleic acid synthesis. These proteins either contain a C-terminal domain that does not mediate allosteric regulation (as in plants) or lack this domain entirely (as in Escherichia coli). As a result, the plant enzymes are not inhibited by S-adenosyl-L-methionine, unlike other eukaryotic enzymes, and catalyse a reversible reaction. cf. EC 1.5.1.53, methylenetetrahydrofolate reductase (NADPH); EC 1.5.1.20, methylenetetrahydrofolate reductase [NAD(P)H]; and EC 1.5.7.1, methylenetetrahydrofolate reductase (ferredoxin).
References:
1. Wohlfarth, G., Geerligs, G. and Diekert, G. Purification and properties of a NADH-dependent 5,10-methylenetetrahydrofolate reductase from Peptostreptococcus productus. Eur. J. Biochem. 192 (1990) 411-417. [PMID: 2209595]
2. Sheppard, C.A., Trimmer, E.E. and Matthews, R.G. Purification and properties of NADH-dependent 5,10-methylenetetrahydrofolate reductase (MetF) from Escherichia coli. J. Bacteriol. 181 (1999) 718-725. [PMID: 9922232]
3. Guenther, B.D., Sheppard, C.A., Tran, P., Rozen, R., Matthews, R.G. and Ludwig, M.L. The structure and properties of methylenetetrahydrofolate reductase from Escherichia coli suggest how folate ameliorates human hyperhomocysteinemia. Nat. Struct. Biol. 6 (1999) 359-365. [PMID: 10201405]
4. Roje, S., Wang, H., McNeil, S.D., Raymond, R.K., Appling, D.R., Shachar-Hill, Y., Bohnert, H.J. and Hanson, A.D. Isolation, characterization, and functional expression of cDNAs encoding NADH-dependent methylenetetrahydrofolate reductase from higher plants. J. Biol. Chem. 274 (1999) 36089-36096. [PMID: 10593891]
5. Bertsch, J., Oppinger, C., Hess, V., Langer, J.D. and Muller, V. Heterotrimeric NADH-oxidizing methylenetetrahydrofolate reductase from the acetogenic bacterium Acetobacterium woodii. J. Bacteriol. 197 (2015) 1681-1689. [PMID: 25733614]
Accepted name: methylenetetrahydrofolate reductase (ferredoxin)
Reaction: 5-methyltetrahydrofolate + 2 oxidized ferredoxin = 5,10-methylenetetrahydrofolate + 2 reduced ferredoxin + 2 H+
For diagram of reaction click here
Other name(s): 5,10-methylenetetrahydrofolate reductase
Systematic name: 5-methyltetrahydrofolate:ferredoxin oxidoreductase
Comments: An iron-sulfur flavoprotein that also contains zinc. The enzyme from Clostridium formicoaceticum catalyses the reduction of methylene blue, menadione, benzyl viologen, rubredoxin or FAD with 5-methyltetrahydrofolate and the oxidation of reduced ferredoxin or FADH2 with 5,10-methylenetetrahydrofolate. However, unlike EC 1.5.1.53, methylenetetrahydrofolate reductase (NADPH); EC 1.5.1.54, methylenetetrahydrofolate reductase (NADH); or EC 1.5.1.20, methylenetetrahydrofolate reductase [NAD(P)H], there is no activity with either NADH or NADP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Clark, J.E. and Ljungdahl, L.G. Purification and properties of 5,10-methylenetetrahydrofolate reductase, an iron-sulfur flavoprotein from Clostridium formicoaceticum. J. Biol. Chem. 259 (1984) 10845-10849. [PMID: 6381490]
[EC 1.10.2.1 Deleted entry: L-ascorbate—cytochrome-b5 reductase. The activity is covered by EC 7.2.1.3, ascorbate ferrireductase (transmembrane) (EC 1.10.2.1 created 1972, modified 2000, deleted 2021)]
[EC 1.14.13.106 Transferred entry: epi-isozizaene 5-monooxygenase, now classified as EC 1.14.15.39, epi-isozizaene 5-monooxygenase. (EC 1.14.13.106 created 2008, deleted 2021)]
Accepted name: ultra-long-chain fatty acid ω-hydroxylase
Reaction: an ultra-long-chain fatty acid + [reduced NADPH—hemoprotein reductase] + O2 = an ultra-long-chain ω-hydroxy fatty acid + [oxidized NADPH—hemoprotein reductase] + H2O
Other name(s): CYP4F22 (gene name)
Systematic name: ultra-long-chain fatty acid,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (ω-hydroxylating)
Comments: The enzyme, which is expressed in the epidermis of mammals, catalyses the ω-hydroxylation of ultra-long-chain fatty acids (C28 to C36). The products are incorporated into acylceramides, epidermis-specific ceramide species that are very important for skin barrier formation.
References:
1. Ohno, Y., Nakamichi, S., Ohkuni, A., Kamiyama, N., Naoe, A., Tsujimura, H., Yokose, U., Sugiura, K., Ishikawa, J., Akiyama, M. and Kihara, A. Essential role of the cytochrome P450 CYP4F22 in the production of acylceramide, the key lipid for skin permeability barrier formation. Proc. Natl. Acad. Sci. USA 112 (2015) 7707-7712. [PMID: 26056268]
Accepted name: epi-isozizaene 5-monooxygenase
Reaction: (+)-epi-isozizaene + 4 reduced [2Fe-2S] ferredoxin + 4 H+ + 2 O2 = albaflavenone + 4 oxidized [2Fe-2S] ferredoxin + 3 H2O (overall reaction)
(1a) (+)-epi-isozizaene + 2 reduced [2Fe-2S] ferredoxin + 2 H+ + O2 = (5S)-albaflavenol + 2 oxidized [2Fe-2S] ferredoxin + H2O
(1b) (5S)-albaflavenol + 2 reduced [2Fe-2S] ferredoxin + 2 H+ + O2 = albaflavenone + 2 oxidized [2Fe-2S] ferredoxin + 2 H2O
(2a) (+)-epi-isozizaene + 2 reduced [2Fe-2S] ferredoxin + 2 H+ + O2 = (5R)-albaflavenol + 2 oxidized [2Fe-2S] ferredoxin + H2O
(2b) (5R)-albaflavenol + 2 reduced [2Fe-2S] ferredoxin + 2 H+ + O2 = albaflavenone + 2 oxidized [2Fe-2S] ferredoxin + 2 H2O
For diagram of reaction, click here
Glossary: (+)-epi-isozizaene = (3S,3aR,6S)-3,7,7,8-tetramethyl-2,3,4,5,6,7-hexahydro-1H-3a,6-methanoazulene
Other name(s): CYP170A1
Systematic name: (+)-epi-isozizaene,reduced-ferredoxin:oxygen oxidoreductase (5-hydroxylating)
Comments: This cytochrome-P-450 enzyme, from the soil-dwelling bacterium Streptomyces coelicolor A3(2), catalyses two sequential allylic oxidation reactions. The substrate epi-isozizaene, which is formed by the action of EC 4.2.3.37, epi-isozizaene synthase, is first oxidized to yield the epimeric intermediates (5R)-albaflavenol and (5S)-albaflavenol, which can be further oxidized to yield the sesquiterpenoid antibiotic albaflavenone.
References:
1. Zhao, B., Lin, X., Lei, L., Lamb, D.C., Kelly, S.L., Waterman, M.R. and Cane, D.E. Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2). J. Biol. Chem. 283 (2008) 8183-8189. [PMID: 18234666]
Accepted name: decanoyl-[acyl-carrier protein] acetylenase
Reaction: decanoyl-[acyl-carrier protein] + 4 reduced ferredoxin [iron-sulfur] cluster + 2 O2 + 4 H+ = dec-9-ynoyl-[acyl-carrier protein] + 4 oxidized ferredoxin [iron-sulfur] cluster + 4 H2O (overall reaction)
(1a) decanoyl-[acyl-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = dec-9-enoyl-[acyl-carrier protein] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
(1b) dec-9-enoyl-[acyl-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = dec-9-ynoyl-[acyl-carrier protein] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
Other name(s): ttuB (gene name) (ambiguous)
Systematic name: decanoyl-[acyl-carrier protein],reduced ferredoxin:oxygen oxidoreductase (9,10-dehydrogenating)
Comments: The enzyme, characterized from the bacterium Teredinibacter turnerae, is specific for decanoyl-[acyl-carrier protein]. Activity is maximal when decanoate is loaded onto a dedicated acyl-carrier protein (TtuC), which is encoded by a gene in the same operon.
References:
1. Zhu, X., Su, M., Manickam, K. and Zhang, W. Bacterial genome mining of enzymatic tools for alkyne biosynthesis. ACS Chem. Biol. 10 (2015) 2785-2793. [PMID: 26441143]
Accepted name: NNS virus cap methyltransferase
Reaction: 2 S-adenosyl-L-methionine + G(5')pppAACA-[mRNA] = 2 S-adenosyl-L-homocysteine + m7G(5')pppAmACA-[mRNA] (overall reaction)
(1a) S-adenosyl-L-methionine + G(5')pppAACA-[mRNA] = S-adenosyl-L-homocysteine + G(5')pppAmACA-[mRNA]
(1b) S-adenosyl-L-methionine + G(5')pppAmACA-[mRNA] = S-adenosyl-L-homocysteine + m7G(5')pppAmACA-[mRNA]
Systematic name: S-adenosyl-L-methionine:G(5')pppAACA-[mRNA] N7,2'-O-methyltransferase
Comments: The enzyme from non-segmented negative strain (NNS) viruses (e.g. rhabdoviruses) catalyses two successive methylations. In higher eukaryotes the two methylations occur in the reverse order and are catalysed by two different enzymes (cf. EC 2.1.1.56, mRNA (guanine-N7)-methyltransferase, and EC 2.1.1.57, methyltransferase cap1) that do not required a specific motif.
References:
1. Rahmeh, A.A., Li, J., Kranzusch, P.J. and Whelan, S.P. Ribose 2'-O methylation of the vesicular stomatitis virus mRNA cap precedes and facilitates subsequent guanine-N-7 methylation by the large polymerase protein. J. Virol. 83 (2009) 11043-11050. [PMID: 19710136]
Accepted name: phosphoribosylglycinamide formyltransferase 1
Reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide
For diagram of reaction click here
Other name(s): 2-amino-N-ribosylacetamide 5'-phosphate transformylase; GAR formyltransferase; GAR transformylase; glycinamide ribonucleotide transformylase; GAR TFase; 5,10-methenyltetrahydrofolate:2-amino-N-ribosylacetamide ribonucleotide transformylase; purN (gene name); ADE8 (gene name); GART (gene name); 5'-phosphoribosylglycinamide transformylase; phosphoribosylglycinamide formyltransferase (ambiguous)
Systematic name: 10-formyltetrahydrofolate:5'-phosphoribosylglycinamide N-formyltransferase
Comments: Two enzymes are known to catalyse the third step in de novo purine biosynthesis. This enzyme utilizes 10-formyltetrahydrofolate as the formyl donor, while the other enzyme, EC 6.3.1.21, phosphoribosylglycinamide formyltransferase 2, utilizes formate. In vertebrates this activity is catalysed by a trifunctional enzyme that also catalyses the activities of EC 6.3.4.13, phosphoribosylamine—glycine ligase and EC 6.3.3.1, phosphoribosylformylglycinamidine cyclo-ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-02-4
References:
1. Hartman, S.C. and Buchanan, J.M. Biosynthesis of the purines. XXVI. The identification of the formyl donors of the transformylation reaction. J. Biol. Chem. 234 (1959) 1812-1816. [PMID: 13672969]
2. Smith, G.K., Benkovic, P.A. and Benkovic, S.J. L(–)-10-Formyltetrahydrofolate is the cofactor for glycinamide ribonucleotide transformylase from chicken liver. Biochemistry 20 (1981) 4034-4036. [PMID: 7284307]
3. Warren, L. and Buchanan, J.M. Biosynthesis of the purines. XIX. 2-Amino-N-ribosylacetamide 5'-phosphate (glycinamide ribotide) transformylase. J. Biol. Chem. 229 (1957) 613-626. [PMID: 13502326]
4. Schild, D., Brake, A.J., Kiefer, M.C., Young, D. and Barr, P.J. Cloning of three human multifunctional de novo purine biosynthetic genes by functional complementation of yeast mutations. Proc. Natl. Acad. Sci. USA 87 (1990) 2916-2920. [PMID: 2183217]
5. Zhang, Y., Desharnais, J., Greasley, S.E., Beardsley, G.P., Boger, D.L. and Wilson, I.A. Crystal structures of human GAR Tfase at low and high pH and with substrate β-GAR. Biochemistry 41 (2002) 14206-14215. [PMID: 12450384]
Accepted name: 6-deoxy-6-sulfo-D-fructose transaldolase
Reaction: 6-deoxy-6-sulfo-D-fructose + D-glyceraldehyde 3-phosphate = (2S)-3-sulfolactaldehyde + β-D-fructofuranose 6-phosphate
Other name(s): sftT (gene name)
Systematic name: 6-deoxy-6-sulfo-D-fructose:D-glyceraldehyde-3-phosphate glyceronetransferase
Comments: The enzyme, characterized from the bacterium Bacillus aryabhattai SOS1, is involved in a degradation pathway for 6-sulfo-D-quinovose. The enzyme can also use D-erythrose 4-phosphate as the acceptor, forming D-sedoheptulose 7-phosphate.
References:
1. Frommeyer, B., Fiedler, A.W., Oehler, S.R., Hanson, B.T., Loy, A., Franchini, P., Spiteller, D. and Schleheck, D. Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway. iScience 23 (2020) 101510. [PMID: 32919372]
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase III
Reaction: acetyl-CoA + a malonyl-[acyl-carrier protein] = an acetoacetyl-[acyl-carrier protein] + CoA + CO2
Other name(s): 3-oxoacyl:ACP synthase III; 3-ketoacyl-acyl carrier protein synthase III; KASIII; KAS III; FabH; β-ketoacyl-acyl carrier protein synthase III; β-ketoacyl-ACP synthase III; β-ketoacyl (acyl carrier protein) synthase III; acetyl-CoA:malonyl-[acyl-carrier-protein] C-acyltransferase
Systematic name: acetyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating straight-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system that occurs in plants and bacteria. In contrast to EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, and EC 2.3.1.179, β-ketoacyl-[acyl-carrier-protein] synthase II, this enzyme specifically uses short-chain acyl-CoA thioesters (preferably acetyl-CoA) rather than acyl-[acp] as its substrate [1]. The enzyme can also catalyse the reaction of EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, but to a much lesser extent [1]. The enzymes from some organisms (e.g. the Gram-positive bacterium Streptococcus pneumoniae) can accept branched-chain acyl-CoAs in addition to acetyl-CoA [5] (cf. EC 2.3.1.300, branched-chain β-ketoacyl-[acyl-carrier-protein] synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1048646-78-1
References:
1. Tsay, J.T., Oh, W., Larson, T.J., Jackowski, S. and Rock, C.O. Isolation and characterization of the β-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12. J. Biol. Chem. 267 (1992) 6807-6814. [PMID: 1551888]
2. Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612-636.
3. Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481-4486. [PMID: 9721286]
4. Choi, K.H., Kremer, L., Besra, G.S. and Rock, C.O. Identification and substrate specificity of β-ketoacyl (acyl carrier protein) synthase III (mtFabH) from Mycobacterium tuberculosis. J. Biol. Chem. 275 (2000) 28201-28207. [PMID: 10840036]
5. Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024-30030. [PMID: 11375394]
6. Qiu, X., Choudhry, A.E., Janson, C.A., Grooms, M., Daines, R.A., Lonsdale, J.T. and Khandekar, S.S. Crystal structure and substrate specificity of the β-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus. Protein Sci. 14 (2005) 2087-2094. [PMID: 15987898]
7. Li, Y., Florova, G. and Reynolds, K.A. Alteration of the fatty acid profile of Streptomyces coelicolor by replacement of the initiation enzyme 3-ketoacyl acyl carrier protein synthase III (FabH). J. Bacteriol. 187 (2005) 3795-3799. [PMID: 15901703]
Accepted name: 3-hydroxy-5-phosphooxypentane-2,4-dione thiolase
Reaction: glycerone phosphate + acetyl-CoA = 3-hydroxy-2,4-dioxopentyl phosphate + CoA
Glossary: (4S)-4,5-dihydroxypentane-2,3-dione = autoinducer 2 = AI-2
Other name(s): lsrF (gene name); 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase
Systematic name: acetyl-CoA:glycerone phosphate C-acetyltransferase
Comments: The enzyme participates in a degradation pathway of the bacterial quorum-sensing autoinducer molecule AI-2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Diaz, Z., Xavier, K.B. and Miller, S.T. The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. PLoS One 4 (2009) e6820. [PMID: 19714241]
2. Marques, J.C., Oh, I.K., Ly, D.C., Lamosa, P., Ventura, M.R., Miller, S.T. and Xavier, K.B. LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2. Proc. Natl. Acad. Sci. USA 111 (2014) 14235-14240. [PMID: 25225400]
Accepted name: branched-chain β-ketoacyl-[acyl-carrier-protein] synthase
Reaction: (1) 3-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a 5-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
(2) 2-methylpropanoyl-CoA + a malonyl-[acyl-carrier protein] = a 4-methyl-3-oxopentanoyl-[acyl-carrier-protein] + CoA + CO2
(3) (2S)-2-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a (4S)-4-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
Glossary: 3-methylbutanoyl-CoA = isovaleryl-CoA
2-methylpropanoyl-CoA = isobutanoyl-CoA = isobutyryl-CoA
Systematic name: 3-methylbutanoyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating branched-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system (FAS-II) in some bacteria, using molecules derived from degradation of the branched-chain amino acids L-leucine, L-valine, and L-isoleucine to form the starting molecules for elongation by the FAS-II system. In some organisms the enzyme is also able to use acetyl-CoA, leading to production of a mix of branched-chain and straight-chain fatty acids [3] (cf. EC 2.3.1.180, β-ketoacyl-[acyl-carrier-protein] synthase III).
References:
1. Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481-4486. [PMID: 9721286]
2. Choi, K.H., Heath, R.J. and Rock, C.O. β-ketoacyl-acyl carrier protein synthase III (FabH) is a determining factor in branched-chain fatty acid biosynthesis. J. Bacteriol. 182 (2000) 365-370. [PMID: 10629181]
3. Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024-30030. [PMID: 11375394]
4. Singh, A.K., Zhang, Y.M., Zhu, K., Subramanian, C., Li, Z., Jayaswal, R.K., Gatto, C., Rock, C.O. and Wilkinson, B.J. FabH selectivity for anteiso branched-chain fatty acid precursors in low-temperature adaptation in Listeria monocytogenes. FEMS Microbiol. Lett. 301 (2009) 188-192. [PMID: 19863661]
5. Yu, Y.H., Hu, Z., Dong, H.J., Ma, J.C. and Wang, H.H. Xanthomonas campestris FabH is required for branched-chain fatty acid and DSF-family quorum sensing signal biosynthesis. Sci. Rep. 6 (2016) 32811. [PMID: 27595587]
Accepted name: mycobacterial β-ketoacyl-[acyl carrier protein] synthase III
Reaction: dodecanoyl-CoA + a malonyl-[acyl-carrier protein] = a 3-oxotetradecanoyl-[acyl-carrier protein] + CoA + CO2
Glossary: dodecanoyl-CoA = lauroyl-CoA
Other name(s): fabH (gene name) (ambiguous); mycobacterial 3-oxoacyl-[acyl carrier protein] synthase III
Systematic name: dodecanoyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme, characterized from mycobacteria, provides a link between the type I and type II fatty acid synthase systems (FAS-I and FAS-II, respectively) found in these organisms. The enzyme acts on medium- and long-chain acyl-CoAs (C12-C16) produced by the FAS-I system, condensing them with malonyl-[acyl-carrier protein] (malonyl-AcpM) and forming starter molecules for the FAS-II system, which elongates them into meromycolic acids. The enzyme has no activity with short-chain acyl-CoAs (e.g. acetyl-CoA), which are used by EC 2.3.1.180, β-ketoacyl-[acyl-carrier-protein] synthase III, or branched-chain acyl-CoAs, which are used by EC 2.3.1.300, branched-chain β-ketoacyl-[acyl-carrier-protein] synthase.
References:
1. Scarsdale, J.N., Kazanina, G., He, X., Reynolds, K.A. and Wright, H.T. Crystal structure of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III. J. Biol. Chem. 276 (2001) 20516-20522. [PMID: 11278743]
2. Musayev, F., Sachdeva, S., Scarsdale, J.N., Reynolds, K.A. and Wright, H.T. Crystal structure of a substrate complex of Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III (FabH) with lauroyl-coenzyme A. J. Mol. Biol. 346 (2005) 1313-1321. [PMID: 15713483]
3. Brown, A.K., Sridharan, S., Kremer, L., Lindenberg, S., Dover, L.G., Sacchettini, J.C. and Besra, G.S. Probing the mechanism of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III mtFabH: factors influencing catalysis and substrate specificity. J. Biol. Chem. 280 (2005) 32539-32547. [PMID: 16040614]
4. Sachdeva, S., Musayev, F.N., Alhamadsheh, M.M., Scarsdale, J.N., Wright, H.T. and Reynolds, K.A. Separate entrance and exit portals for ligand traffic in Mycobacterium tuberculosis FabH. Chem. Biol. 15 (2008) 402-412. [PMID: 18420147]
Accepted name: hydroxycinnamoyl-CoA:5-hydroxyanthranilate N-hydroxycinnamoyltransferase
Reaction: (1) (E)-4-coumaroyl-CoA + 5-hydroxyanthranilate = avenanthramide A + CoA
(2) (E)-caffeoyl-CoA + 5-hydroxyanthranilate = avenanthramide C + CoA
Glossary: avenanthramide A = 5-hydroxy-2-[(2E)-3-(4-hydroxyphenyl)prop-2-enamido]benzoate
avenanthramide C = 2-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enamido]-5-hydroxybenzoate
Other name(s): HHT1 (gene name); HHT4 (gene name)
Systematic name: hydroxycinnamoyl-CoA:5-hydroxyanthranilate N-hydroxycinnamoyltransferase
Comments: The enzyme participates in the biosynthesis of avenanthramides, phenolic alkaloids found mainly in oats (Avena sativa). It is related to EC 2.3.1.133, shikimate O-hydroxycinnamoyltransferase. The enzyme from oat does not accept feruloyl-CoA as a substrate.
References:
1. Ishihara, A., Matsukawa, T., Miyagawa, H., Ueno, T. and Mayama, S. Induction of hydroxycinnamoyl-CoA: hydroxyanthranilate N-hydroxycinnamoyltransferase (HHT) activity in oat leaves by victorin C. Z. Naturforsch. C 52 (1997) 756-760.
2. Yang, Q., Trinh, H.X., Imai, S., Ishihara, A., Zhang, L., Nakayashiki, H., Tosa, Y. and Mayama, S. Analysis of the involvement of hydroxyanthranilate hydroxycinnamoyltransferase and caffeoyl-CoA 3-O-methyltransferase in phytoalexin biosynthesis in oat. Mol. Plant Microbe Interact. 17 (2004) 81-89. [PMID: 14714871]
3. D'Auria, J.C. Acyltransferases in plants: a good time to be BAHD. Curr. Opin. Plant Biol. 9 (2006) 331-340. [PMID: 16616872]
4. Bontpart, T., Cheynier, V., Ageorges, A. and Terrier, N. BAHD or SCPL acyltransferase? What a dilemma for acylation in the world of plant phenolic compounds. New Phytol. 208 (2015) 695-707. [PMID: 26053460]
5. Li, Z., Chen, Y., Meesapyodsuk, D. and Qiu, X. The biosynthetic pathway of major avenanthramides in oat. Metabolites 9 (2019) . [PMID: 31394723]
Accepted name: α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und 2IV-O-acetyltransferase
Reaction: acetyl-CoA + α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = CoA + 2-O-acetyl-α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und
Glossary: α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): rfbL (gene name); wbaL (gene name)
Systematic name: acetyl-CoA:α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 2IV-O-acetyltransferase
Comments: The enzyme, present in Salmonella strains that belong to group C2, participates in the biosynthesis of the repeat unit of O antigens produced by these strains.
References:
1. Brown, P.K., Romana, L.K. and Reeves, P.R. Molecular analysis of the rfb gene cluster of Salmonella serovar muenchen (strain M67): the genetic basis of the polymorphism between groups C2 and B. Mol. Microbiol. 6 (1992) 1385-1394. [PMID: 1379320]
2. Liu, D., Lindqvist, L. and Reeves, P.R. Transferases of O-antigen biosynthesis in Salmonella enterica: dideoxyhexosyltransferases of groups B and C2 and acetyltransferase of group C2. J. Bacteriol. 177 (1995) 4084-4088. [PMID: 7541787]
3. Zhao, X., Dai, Q., Jia, R., Zhu, D., Liu, M., Wang, M., Chen, S., Sun, K., Yang, Q., Wu, Y. and Cheng, A. two novel Salmonella bivalent vaccines confer dual protection against two Salmonella serovars in mice. Front Cell Infect Microbiol 7 (2017) 391. [PMID: 28929089]
Accepted name: CDP-abequose:α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und α-1,3-abequosyltransferase
Reaction: CDP-α-D-abequose + α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = CDP + α-D-Abe-(1→3)-α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und
Glossary: D-abequose = 3,6-deoxy-D-xylo-hexose = 3,6-deoxy-D-galactose = 3-deoxy-D-fucose
α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-D-Abe-(1→3)-α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-D-abequopyranosyl-(1→3)-α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaV (gene name); rfbV (gene name); trihexose diphospholipid abequosyltransferase; abequosyltransferase (ambiguous); CDP-α-D-abequose:Man(α1→4)Rha(α1→3)Gal(β-1)-diphospholipid D-abequosyltransferase
Systematic name: CDP-α-D-abequose:α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 3III-α-abequosyltransferase (configuration retaining)
Comments: The enzyme from Salmonella participates in the biosynthesis of the repeat unit of O antigens produced by strains that belong to the A, B and D1-D3 groups. The enzyme is able to transfer abequose, paratose, or tyvelose, depending on the availability of the specific dideoxyhexose in a particular strain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37277-67-1
References:
1. Osborn, M.J. and Weiner, I.M. Biosynthesis of a bacterial lipopolysaccharide. VI. Mechanism of incorporation of abequose into the O-antigen of Salmonella typhimurium. J. Biol. Chem. 243 (1968) 2631-2639. [PMID: 4297268]
2. Liu, D., Lindqvist, L. and Reeves, P.R. Transferases of O-antigen biosynthesis in Salmonella enterica: dideoxyhexosyltransferases of groups B and C2 and acetyltransferase of group C2. J. Bacteriol. 177 (1995) 4084-4088. [PMID: 7541787]
Accepted name: dTDP-Rha:α-D-Gal-diphosphoundecaprenol α-1,3-rhamnosyltransferase
Reaction: dTDP-β-L-rhamnose + α-D-galactosyl-diphospho-ditrans,octacis-undecaprenol = dTDP + α-L-Rha-(1→3)-α-D-Gal-PP-Und
Glossary: α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaN (gene name); rfbN (gene name)
Systematic name: dTDP-β-L-rhamnose:α-D-galactosyl-diphospho-ditrans,octacis-undecaprenol 3-α-rhamnosyltransferase (configuration-inverting)
Comments: The enzyme, characterized from several Salmonella strains, participates in the biosynthesis of the repeat unit of O antigens produced by strains that belong to the A, B, D and E groups.
References:
1. Liu, D., Haase, A.M., Lindqvist, L., Lindberg, A.A. and Reeves, P.R. Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. J. Bacteriol. 175 (1993) 3408-3413. [PMID: 7684736]
Accepted name: GDP-mannose:α-L-Rha-(1→3)-α-D-Gal-PP-Und α-1,4-mannosyltransferase
Reaction: GDP-α-D-mannose + α-L-Rha-(1→3)-α-D-Gal-PP-Und = GDP + α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und
Glossary: α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaU (gene name); rfbU (gene name)
Systematic name: GDP-α-D-mannose:α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 4II-α-rhamnosyltransferase (configuration-retaining)
Comments: The enzyme from Salmonella participates in the biosynthesis of the repeat unit of O antigens produced by strains that belong to the A, B, and D1 groups.
References:
1. Liu, D., Haase, A.M., Lindqvist, L., Lindberg, A.A. and Reeves, P.R. Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. J. Bacteriol. 175 (1993) 3408-3413. [PMID: 7684736]
Accepted name: GDP-Man:α-D-Gal-diphosphoundecaprenol α-1,3-mannosyltransferase
Reaction: GDP-α-D-mannose + α-D-galactosyl-diphospho-ditrans-octacis-undecaprenol = GDP + α-D-Man-(1→3)-α-D-Gal-PP-Und
Glossary: α-D-Man-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaZ (gene name); rfbZ (gene name)
Systematic name: GDP-α-D-mannose:α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 3-α-mannosyltransferase (configuration-retaining)
Comments: The enzyme, present in Salmonella strains that belong to group C2, participates in the biosynthesis of the repeat unit of O antigens produced by these strains.
References:
1. Brown, P.K., Romana, L.K. and Reeves, P.R. Cloning of the rfb gene cluster of a group C2 Salmonella strain: comparison with the rfb regions of groups B and D. Mol. Microbiol. 5 (1991) 1873-1881. [PMID: 1722557]
2. Brown, P.K., Romana, L.K. and Reeves, P.R. Molecular analysis of the rfb gene cluster of Salmonella serovar muenchen (strain M67): the genetic basis of the polymorphism between groups C2 and B. Mol. Microbiol. 6 (1992) 1385-1394. [PMID: 1379320]
3. Liu, D., Haase, A.M., Lindqvist, L., Lindberg, A.A. and Reeves, P.R. Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. J. Bacteriol. 175 (1993) 3408-3413. [PMID: 7684736]
4. Zhao, X., Dai, Q., Jia, R., Zhu, D., Liu, M., Wang, M., Chen, S., Sun, K., Yang, Q., Wu, Y. and Cheng, A. two novel Salmonella bivalent vaccines confer dual protection against two Salmonella serovars in mice. Front Cell Infect Microbiol 7 (2017) 391. [PMID: 28929089]
Accepted name: GDP-Man:α-D-Man-(1→3)-α-D-Gal diphosphoundecaprenol α-1,2-mannosyltransferase
Reaction: GDP-α-D-mannose + α-D-Man-(1→3)-α-D-Gal-PP-Und = GDP + α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und
Glossary: α-D-Man-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaW (gene name); rfbW (gene name)
Systematic name: GDP-α-D-mannose:α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 2II-α-mannosyltransferase
Comments: The enzyme, present in Salmonella strains that belong to group C2, participates in the biosynthesis of the repeat unit of O antigens produced by these strains.
References:
1. Brown, P.K., Romana, L.K. and Reeves, P.R. Cloning of the rfb gene cluster of a group C2 Salmonella strain: comparison with the rfb regions of groups B and D. Mol. Microbiol. 5 (1991) 1873-1881. [PMID: 1722557]
2. Brown, P.K., Romana, L.K. and Reeves, P.R. Molecular analysis of the rfb gene cluster of Salmonella serovar muenchen (strain M67): the genetic basis of the polymorphism between groups C2 and B. Mol. Microbiol. 6 (1992) 1385-1394. [PMID: 1379320]
3. Liu, D., Haase, A.M., Lindqvist, L., Lindberg, A.A. and Reeves, P.R. Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. J. Bacteriol. 175 (1993) 3408-3413. [PMID: 7684736]
Accepted name: dTDP-Rha:α-D-Man-(1→3)-α-D-Gal diphosphoundecaprenol α-1,2-rahmnosyltransferase
Reaction: dTDP-β-L-rhamnose + α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = dTDP + α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und
Glossary: α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaQ (gene name); rfbQ (gene name)
Systematic name: dTDP-β-L-rhamnose:α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 2III-α-rhamnosyltransferase (configuration inverting)
Comments: The enzyme, present in Salmonella strains that belong to group C2, participates in the biosynthesis of the repeat unit of O antigens produced by these strains.
References:
1. Brown, P.K., Romana, L.K. and Reeves, P.R. Cloning of the rfb gene cluster of a group C2 Salmonella strain: comparison with the rfb regions of groups B and D. Mol. Microbiol. 5 (1991) 1873-1881. [PMID: 1722557]
2. Brown, P.K., Romana, L.K. and Reeves, P.R. Molecular analysis of the rfb gene cluster of Salmonella serovar muenchen (strain M67): the genetic basis of the polymorphism between groups C2 and B. Mol. Microbiol. 6 (1992) 1385-1394. [PMID: 1379320]
3. Liu, D., Haase, A.M., Lindqvist, L., Lindberg, A.A. and Reeves, P.R. Glycosyl transferases of O-antigen biosynthesis in Salmonella enterica: identification and characterization of transferase genes of groups B, C2, and E1. J. Bacteriol. 175 (1993) 3408-3413. [PMID: 7684736]
4. Zhao, X., Dai, Q., Jia, R., Zhu, D., Liu, M., Wang, M., Chen, S., Sun, K., Yang, Q., Wu, Y. and Cheng, A. two novel Salmonella bivalent vaccines confer dual protection against two Salmonella serovars in mice. Front Cell Infect Microbiol 7 (2017) 391. [PMID: 28929089]
Accepted name: CDP-abequose:α-L-Rha2OAc-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und α-1,3-abequosyltransferase
Reaction: CDP-α-D-abequose + 2-O-acetyl-α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = CDP + α-D-Abe-(1→3)-2-O-acetyl-α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und
Glossary: α-L-Rha2OAc-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = 2-O-acetyl-α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
α-D-Abe-(1→3)-2-O-acetyl-α-L-Rha-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Gal-PP-Und = α-D-abequosyl-(1→3)-2-O-acetyl-α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaR (gene name); rfbR (gene name)
Systematic name: CDP-α-D-abequose:2-O-acetyl-α-L-rhamnopyranosyl-(1→2)-α-D-mannopyranosyl-(1→2)-α-D-mannopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 3IV-α-abequosyltransferase (configuration retaining)
Comments: The enzyme, present in Salmonella strains that belong to group C2, participates in the biosynthesis of the repeat unit of O antigens produced by these strains.
References:
1. Liu, D., Lindqvist, L. and Reeves, P.R. Transferases of O-antigen biosynthesis in Salmonella enterica: dideoxyhexosyltransferases of groups B and C2 and acetyltransferase of group C2. J. Bacteriol. 177 (1995) 4084-4088. [PMID: 7541787]
2. Zhao, X., Dai, Q., Jia, R., Zhu, D., Liu, M., Wang, M., Chen, S., Sun, K., Yang, Q., Wu, Y. and Cheng, A. two novel Salmonella bivalent vaccines confer dual protection against two Salmonella serovars in mice. Front Cell Infect Microbiol 7 (2017) 391. [PMID: 28929089]
Accepted name: GDP-Man:α-L-Rha-(1→3)-α-D-Gal-PP-Und β-1,4-mannosyltransferase
Reaction: GDP-α-D-mannose + α-L-Rha-(1→3)-α-D-Gal-PP-Und = GDP + β-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und
Glossary: α-L-Rha-(1→3)-α-D-Gal-PP-Und = α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
β-D-Man-(1→4)-α-L-Rha-(1→3)-α-D-Gal-PP-Und = β-D-mannopyranosyl-(1→4)-α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): wbaO (gene name); rfbO (gene name)
Systematic name: GDP-α-D-mannose:α-L-rhamnopyranosyl-(1→3)-α-D-galactopyranosyl-diphospho-ditrans,octacis-undecaprenol 4II-β-mannosyltransferase (configuration inverting)
Comments: The enzyme participates in the biosynthesis of the O antigens produced by group E and D2 strains of the pathogenic bacterium Salmonella enterica.
References:
1. Xiang, S.H., Hobbs, M. and Reeves, P.R. Molecular analysis of the rfb gene cluster of a group D2 Salmonella enterica strain: evidence for its origin from an insertion sequence-mediated recombination event between group E and D1 strains. J. Bacteriol. 176 (1994) 4357-4365. [PMID: 8021222]
2. Zhao, Y., Biggins, J. B. and Thorson, J. S. Acceptor specificity of Salmonella GDP-Man:α-L-Rha-(1→3)-α-D- Gal- PP-Und β(1→4)-mannosyltransferase: A simplified assay based on unnatural acceptors. J. Am. Chem. Soc. 120 (1998) 12986-12987.
3. Zhao, Y. and Thorson, J.S. Chemoenzymatic synthesis of the Salmonella group E1 core trisaccharide using a recombinant β-(1-→4)-mannosyltransferase. Carbohydr. Res. 319 (1999) 184-191. [PMID: 10520265]
Accepted name: levoglucosan kinase
Reaction: ATP + levoglucosan + H2O = ADP + D-glucose 6-phosphate
Glossary: levoglucosan = 1,6-anhydro-β-D-glucopyranose
Systematic name: ATP:1,6-anhydro-β-D-glucopyranose 6-phosphotransferase (hydrolyzing)
Comments: Levoglucosan is formed from the pyrolysis of carbohydrates such as starch and cellulose and is an important molecular marker for pollution from biomass burning. The enzyme, found in yeast and fungi, requires a magnesium ion. cf. EC 1.1.1.425, levoglucosan dehydrogenase.
References:
1. Zhuang, X. and Zhang, H. Identification, characterization of levoglucosan kinase, and cloning and expression of levoglucosan kinase cDNA from Aspergillus niger CBX-209 in Escherichia coli. Protein Expr. Purif. 26 (2002) 71-81. [PMID: 12356473]
2. Dai, J., Yu, Z., He, Y., Zhang, L., Bai, Z., Dong, Z., Du, Y. and Zhang, H. Cloning of a novel levoglucosan kinase gene from Lipomyces starkeyi and its expression in Escherichia coli. World J. Microbiol. Biotechnol. 25 (2009) 1589-1595.
3. Layton, D.S., Ajjarapu, A., Choi, D.W. and Jarboe, L.R. Engineering ethanologenic Escherichia coli for levoglucosan utilization. Bioresour. Technol. 102 (2011) 8318-8322. [PMID: 21719279]
4. Islam, Z.U., Zhisheng, Y., Hassan el, B., Dongdong, C. and Hongxun, Z. Microbial conversion of pyrolytic products to biofuels: a novel and sustainable approach toward second-generation biofuels. J. Ind. Microbiol. Biotechnol. 42 (2015) 1557-1579. [PMID: 26433384]
5. Bacik, J.P., Klesmith, J.R., Whitehead, T.A., Jarboe, L.R., Unkefer, C.J., Mark, B.L. and Michalczyk, R. Producing glucose 6-phosphate from cellulosic biomass: structural insights into levoglucosan bioconversion. J. Biol. Chem. 290 (2015) 26638-26648. [PMID: 26354439]
Accepted name: ATP-polyphosphate phosphotransferase
Reaction: ATP + (phosphate)n = ADP + (phosphate)n+1
Other name(s): polyphosphate kinase 1; ppk1 (gene name); polyphosphate kinase (ambiguous); polyphosphoric acid kinase (ambiguous)
Systematic name: ATP:polyphosphate phosphotransferase
Comments: The enzyme is responsible for the synthesis of most of the cellular polyphosphate, using the terminal phosphate of ATP as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-44-2
References:
1. Hoffmann-Ostenhof, O., Kenedy, J., Keck, K., Gabriel, O. and Schönfellinger, H.W. En neues Phosphat-übertragendes Ferment aus Hefe. Biochim. Biophys. Acta 14 (1954) 285. [PMID: 13172250]
2. Kornberg, A., Kornberg, S.R. and Simms, E.S. Metaphosphate synthesis by an enzyme from Escherichia coli. Biochim. Biophys. Acta 20 (1956) 215-227. [PMID: 13315368]
3. Muhammed, A. Studies on biosynthesis of polymetaphosphate by an enzyme from Corynebacterium xerosis. Biochim. Biophys. Acta 54 (1961) 121-132. [PMID: 14476999]
4. Ahn, K. and Kornberg, A. Polyphosphate kinase from Escherichia coli. Purification and demonstration of a phosphoenzyme intermediate. J. Biol. Chem. 265 (1990) 11734-11739. [PMID: 2164013]
5. Kumble, K.D., Ahn, K. and Kornberg, A. Phosphohistidyl active sites in polyphosphate kinase of Escherichia coli. Proc. Natl. Acad. Sci. USA 93 (1996) 14391-14395. [PMID: 8962061]
Accepted name: GDP-polyphosphate phosphotransferase
Reaction: GTP + (phosphate)n = GDP + (phosphate)n+1
Other name(s): ppk2 (gene name); polyphosphate kinase 2
Systematic name: GTP:polyphosphate phosphotransferase
Comments: Polyphosphate kinase 2, characterized from the bacterium Pseudomonas aeruginosa, uses inorganic polyphosphate as a donor to convert GDP to GTP. The enzyme can also act on ADP (cf. EC 2.7.4.1, ATP-polyphosphate phosphotransferase), but with lower activity. The enzyme has only a trivial activity in the opposite direction (synthesizing polyphosphate from GTP). The GTP that is produced is believed to be consumed by EC 2.7.7.13, mannose-1-phosphate guanylyltransferase, for production of alginate during stationary phase.
References:
1. Zhang, H., Ishige, K. and Kornberg, A. A polyphosphate kinase (PPK2) widely conserved in bacteria. Proc. Natl. Acad. Sci. USA 99 (2002) 16678-16683. [PMID: 12486232]
2. Ishige, K., Zhang, H. and Kornberg, A. Polyphosphate kinase (PPK2), a potent, polyphosphate-driven generator of GTP. Proc. Natl. Acad. Sci. USA 99 (2002) 16684-16688. [PMID: 12482933]
Accepted name: mRNA guanylyltransferase
Reaction: GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Glossary: a 5'-(5'-triphosphoguanosine)-[mRNA] = G(5')pppPur-mRNA = mRNA containing a guanosine residue linked 5' through three phosphates to the 5' position of the terminal residue
Other name(s): RNGTT (gene name); CEG1 (gene name); mRNA capping enzyme; messenger RNA guanylyltransferase; Protein λ2
Systematic name: GTP:mRNA guanylyltransferase
Comments: The human enzyme is a multi domain protein that also has the activity of EC 3.6.1.74, mRNA 5'-phosphatase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 56941-23-2
References:
1. Ensinger, M.J., Martin, S.A., Paoletti, E. and Moss, B. Modification of the 5'-terminus of mRNA by soluble guanylyl and methyl transferases from vaccinia virus. Proc. Natl. Acad. Sci. USA 72 (1975) 2525-2529. [PMID: 1058472]
2. Groner, Y., Gilbao, E. and Aviv, H. Methylation and capping of RNA polymerase II primary transcripts by HeLa nuclear homogenates. Biochemistry 17 (1978) 977-982. [PMID: 629955]
3. Itoh, N., Yamada, H., Kaziro, Y. and Mizumoto, K. Messenger RNA guanylyltransferase from Saccharomyces cerevisiae. Large scale purification, subunit functions, and subcellular localization. J. Biol. Chem. 262 (1987) 1989-1995. [PMID: 3029058]
4. Martin, S.A. and Moss, B. Modification of RNA by mRNA guanylyltransferase and mRNA(guanine-7-)methyltransferase from vaccinia virions. J. Biol. Chem. 250 (1975) 9330-9335. [PMID: 1194287]
5. Martin, S.A., Paoletti, E. and Moss, B. Purification of mRNA guanylyltransferase and mRNA(guanine-7-)methyltransferase from vaccinia virions. J. Biol. Chem. 250 (1975) 9322-9329. [PMID: 1194286]
Accepted name: sn-1-specific diacylglycerol lipase
Reaction: a 1,2-diacyl-sn-glycerol + H2O = a 2-acylglycerol + a fatty acid
Other name(s): DAGLA (gene name); DAGLB (gene name)
Systematic name: diacylglycerol sn-1-acylhydrolase
Comments: The enzyme, present in animals, is specific for the sn-1 position. When acting on 1-acyl-2-arachidonoyl-sn-glycerol, the enzyme forms 2-arachidonoylglycerol, the most abundant endocannabinoid in the mammalian brain.
References:
1. Chau, L.Y. and Tau, H.H. Release of arachidonate from diglyceride in human platelets requires the sequential action of a diglyceride lipase and a monoglyceride lipase. Biochem. Biophys. Res. Commun. 100 (1988) 1688-1695. [PMID: 7295321]
2. Bisogno, T., Howell, F., Williams, G., Minassi, A., Cascio, M.G., Ligresti, A., Matias, I., Schiano-Moriello, A., Paul, P., Williams, E.J., Gangadharan, U., Hobbs, C., Di Marzo, V. and Doherty, P. Cloning of the first sn1-DAG lipases points to the spatial and temporal regulation of endocannabinoid signaling in the brain. J. Cell Biol. 163 (2003) 463-468. [PMID: 14610053]
3. Bisogno, T. Assay of DAGLα/β activity. Methods Mol. Biol. 1412 (2016) 149-156. [PMID: 27245901]
Accepted name: (4-O-methyl)-D-glucuronate—lignin esterase
Reaction: a 4-O-methyl-D-glucopyranuronate ester + H2O = 4-O-methyl-D-glucuronic acid + an alcohol
Other name(s): glucuronoyl esterase (ambiguous); 4-O-methyl-glucuronoyl methylesterase; glucuronoyl-lignin ester hydrolase
Systematic name: (4-O-methyl)-D-glucuronate—lignin ester hydrolase
Comments: The enzyme occurs in microorganisms and catalyses the cleavage of the ester bonds between glucuronoyl or 4-O-methyl-glucuronoyl groups attached to xylan and aliphatic or aromatic alcohols in lignin polymers.
References:
1. Spanikova, S. and Biely, P. Glucuronoyl esterase--novel carbohydrate esterase produced by Schizophyllum commune. FEBS Lett. 580 (2006) 4597-4601. [PMID: 16876163]
2. Charavgi, M.D., Dimarogona, M., Topakas, E., Christakopoulos, P. and Chrysina, E.D. The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst. Acta Crystallogr. D Biol. Crystallogr. 69 (2013) 63-73. [PMID: 23275164]
3. Arnling Baath, J., Giummarella, N., Klaubauf, S., Lawoko, M. and Olsson, L. A glucuronoyl esterase from Acremonium alcalophilum cleaves native lignin-carbohydrate ester bonds. FEBS Lett. 590 (2016) 2611-2618. [PMID: 27397104]
4. Huttner, S., Klaubauf, S., de Vries, R.P. and Olsson, L. Characterisation of three fungal glucuronoyl esterases on glucuronic acid ester model compounds. Appl. Microbiol. Biotechnol. 101 (2017) 5301-5311. [PMID: 28429057]
5. Huynh, H.H. and Arioka, M. Functional expression and characterization of a glucuronoyl esterase from the fungus Neurospora crassa: identification of novel consensus sequences containing the catalytic triad. J. Gen. Appl. Microbiol. 62 (2016) 217-224. [PMID: 27600355]
6. Arnling Baath, J., Mazurkewich, S., Knudsen, R.M., Poulsen, J.N., Olsson, L., Lo Leggio, L. and Larsbrink, J. Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion. Biotechnol Biofuels 11 (2018) 213. [PMID: 30083226]
7. Mazurkewich, S., Poulsen, J.N., Lo Leggio, L. and Larsbrink, J. Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components. J. Biol. Chem. 294 (2019) 19978-19987. [PMID: 31740581]
8. Ernst, H.A., Mosbech, C., Langkilde, A.E., Westh, P., Meyer, A.S., Agger, J.W. and Larsen, S. The structural basis of fungal glucuronoyl esterase activity on natural substrates. Nat. Commun. 11 (2020) 1026. [PMID: 32094331]
Accepted name: cyclic 2,3-diphosphoglycerate hydrolase
Reaction: cyclic 2,3-bisphosphoglycerate + H2O = 2,3-diphosphoglycerate
Systematic name: cyclic 2,3-diphosphoglycerate phosphohydrolyase
Comments: The enzyme degrades cyclic 2,3-bisphosphoglycerate, a thermoprotectant that is produced by certain archaeal genera. Two different enzymes that catalyse this activity, one soluble and one membrane-bound, have been characterized from the archaeon Methanothermobacter thermautotrophicus.
References:
1. Sastry, M.V., Robertson, D.E., Moynihan, J.A. and Roberts, M.F. Enzymatic degradation of cyclic 2,3-diphosphoglycerate to 2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum. Biochemistry 31 (1992) 2926-2935. [PMID: 1550819]
2. Alebeek G, J.WM., Kreuwels, M.JJ., Keltjens, J.T. and Vogels, G.D. Methanobacterium thermoautotrophicum (strain ΔH) contains a membrane-bound cyclic 2,3-diphosphoglycerate hydrolase. Arch. Microbiol. 161 (1994) 514-520.
Accepted name: mRNA 5'-phosphatase
Reaction: a 5'-triphospho-[mRNA] + H2O = a 5'-diphospho-[mRNA] + phosphate
Other name(s): 5'-polynucleotidase; polynucleotide 5'-phosphohydrolase; RNGTT (gene name); CET1 (gene name)
Systematic name: 5'-triphospho-mRNA 5'-phosphohydrolase
Comments: The enzyme, found in eukaryotes and some plus strand RNA viruses (e.g. alphavirus), is involved in mRNA capping. Unlike the eukaryotic enzyme, the viral enzyme requires a purine in the first position of the mRNA. The human enzyme is a multi domain protein that also has the activity of EC 2.7.7.50, mRNA guanylyltransferase.
References:
1. Itoh, N., Mizumoto, K. and Kaziro, Y. Messenger RNA guanlyltransferase from Saccharomyces cerevisiae. II. Catalytic properties. J. Biol. Chem. 259 (1984) 13930-13936. [PMID: 6094533]
2. Tsukamoto, T., Shibagaki, Y., Murakoshi, T., Suzuki, M., Nakamura, A., Gotoh, H. and Mizumoto, K. Cloning and characterization of two human cDNAs encoding the mRNA capping enzyme. Biochem. Biophys. Res. Commun. 243 (1998) 101-108. [PMID: 9473487]
3. Vasiljeva, L., Merits, A., Auvinen, P. and Kaariainen, L. Identification of a novel function of the alphavirus capping apparatus. RNA 5'-triphosphatase activity of Nsp2. J. Biol. Chem. 275 (2000) 17281-17287. [PMID: 10748213]
Accepted name: 3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethylpyrrolidin-2-one synthase
Reaction: C-terminal [mycofactocin precursor peptide]-glycyl-3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethylpyrrolidin-2-one + 5'-deoxyadenosine + L-methionine + A = C-terminal [mycofactocin precursor peptide]-glycyl-L-valyl-4-[2-aminoethenyl]phenol + S-adenosyl-L-methionine + AH2
Other name(s): mftC (gene name)
Systematic name: C-terminal [mycofactocin precursor peptide]-glycyl-3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethylpyrrolidin-2-one lyase (C-terminal [mycofactocin precursor peptide]-glycyl-L-valyl-4-[2-aminoethenyl]phenol-forming)
Comments: This is a bifunctional radical AdoMet (radical SAM) enzyme that catalyses the first two steps in the biosynthesis of the enzyme cofactor mycofactocin. Activity requires the presence of the MftB chaperone. The reaction occurs in the right-to-left direction. The other activity of the enzyme is EC 1.3.98.7, [mycofactocin precursor peptide]-tyrosine decarboxylase.
References:
1. Haft, D.H. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. BMC Genomics 12 (2011) 21. [PMID: 21223593]
2. Bruender, N.A. and Bandarian, V. The radical S-adenosyl-L-methionine enzyme MftC catalyzes an oxidative decarboxylation of the C-terminus of the MftA peptide. Biochemistry 55 (2016) 2813-2816. [PMID: 27158836]
3. Khaliullin, B., Ayikpoe, R., Tuttle, M. and Latham, J.A. Mechanistic elucidation of the mycofactocin-biosynthetic radical S-adenosylmethionine protein, MftC. J. Biol. Chem. 292 (2017) 13022-13033. [PMID: 28634235]
4. Ayikpoe, R., Ngendahimana, T., Langton, M., Bonitatibus, S., Walker, L.M., Eaton, S.S., Eaton, G.R., Pandelia, M.E., Elliott, S.J. and Latham, J.A. Spectroscopic and electrochemical characterization of the mycofactocin biosynthetic protein, MftC, provides insight into its redox flipping mechanism. Biochemistry 58 (2019) 940-950. [PMID: 30628436]
Accepted name: 1-aminocyclopropane-1-carboxylate synthase
Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl-5'-thioadenosine
For diagram of reaction click here
Glossary: S-methyl-5'-thioadenosine = 5'-deoxy-5'-(methylsulfanyl)adenosine
Other name(s): 1-aminocyclopropanecarboxylate synthase; 1-aminocyclopropane-1-carboxylic acid synthase; 1-aminocyclopropane-1-carboxylate synthetase; aminocyclopropanecarboxylic acid synthase; aminocyclopropanecarboxylate synthase; ACC synthase; S-adenosyl-L-methionine methylthioadenosine-lyase; S-adenosyl-L-methionine methylthioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Systematic name: S-adenosyl-L-methionine S-methyl-5'-thioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Comments: A pyridoxal 5'-phosphate protein. The enzyme catalyses an α,γ-elimination.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72506-68-4
References:
1. Boller, T., Herner, R.C. and Kende, H. Assay for and enzymatic formation of an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid. Planta 145 (1979) 293-303. [PMID: 24317737]
2. Yu, Y.-B., Adams, D.O. and Yang, S.F. 1-Aminocyclopropanecarboxylate synthase, a key enzyme in ethylene biosynthesis. Arch. Biochem. Biophys. 198 (1979) 280-296. [PMID: 507845]
Accepted name: S-methyl-5-thioribulose 1-phosphate isomerase
Reaction: (1) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-xylulose 5-phosphate
(2) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-ribulose 5-phosphate
Other name(s): rlp (gene name); 5-methylthioribulose-1-phosphate isomerase (incorrect)
Systematic name: S-methyl-5-thio-D-ribulose 1-phosphate 1,3-isomerase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, participates in methionine salvage from S-methyl-5'-thioadenosine. It is a RubisCO-like protein (RLP) that is not capable of carbon fixation, and catalyses an isomerization reaction that converts S-methyl-5-thio-D-ribulose 1-phosphate to a 3:1 mixture of S-methyl-1-thioxylulose 5-phosphate and S-methyl-1-thioribulose 5-phosphate. The reaction is an overall 1,3-proton transfer, which likely consists of two 1,2-proton transfer events.
References:
1. Imker, H.J., Singh, J., Warlick, B.P., Tabita, F.R. and Gerlt, J.A. Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum. Biochemistry 47 (2008) 11171-11173. [PMID: 18826254]
2. Erb, T.J., Evans, B.S., Cho, K., Warlick, B.P., Sriram, J., Wood, B.M., Imker, H.J., Sweedler, J.V., Tabita, F.R. and Gerlt, J.A. A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat. Chem. Biol. 8 (2012) 926-932. [PMID: 23042035]
Accepted name: glyine—[glycyl-carrier protein] ligase
Reaction: ATP + glycine + holo-[glycyl-carrier protein] = AMP + diphosphate + glycyl-[glycyl-carrier protein] (overall reaction)
(1a) ATP + glycine = diphosphate + (glycyl)adenylate
(1b) (glycyl)adenylate + holo-[glycyl-carrier protein] = AMP + glycyl-[glycyl-carrier protein]
Other name(s): dhbF (gene name); sfmB (gene name)
Systematic name: glycine:[glycyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of glycine to (glycyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein (as in the case of DhbF in bacillibactin biosynthesis), or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
References:
1. May, J.J., Wendrich, T.M. and Marahiel, M.A. The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin. J. Biol. Chem. 276 (2001) 7209-7217. [PMID: 11112781]
2. Li, L., Deng, W., Song, J., Ding, W., Zhao, Q.F., Peng, C., Song, W.W., Tang, G.L. and Liu, W. Characterization of the saframycin A gene cluster from Streptomyces lavendulae NRRL 11002 revealing a nonribosomal peptide synthetase system for assembling the unusual tetrapeptidyl skeleton in an iterative manner. J. Bacteriol. 190 (2008) 251-263. [PMID: 17981978]
Accepted name: L-alanine—[L-alanyl-carrier protein] ligase
Reaction: ATP + L-alanine + holo-[L-alanyl-carrier protein] = AMP + diphosphate + L-alanyl-[L-alanyl-carrier protein] (overall reaction)
(1a) ATP + L-alanine = diphosphate + (L-alanyl)adenylate
(1b) (L-alanyl)adenylate + holo-[L-alanyl-carrier protein] = AMP + L-alanyl-[L-alanyl-carrier protein]
Other name(s): ambB (gene name); phsB (gene name)
Systematic name: L-alanine:[L-alanyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-alanine to (L-alanyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
References:
1. Schwartz, D., Grammel, N., Heinzelmann, E., Keller, U. and Wohlleben, W. Phosphinothricin tripeptide synthetases in Streptomyces viridochromogenes Tu494. Antimicrob. Agents Chemother. 49 (2005) 4598-4607. [PMID: 16251301]
2. Rojas Murcia, N., Lee, X., Waridel, P., Maspoli, A., Imker, H.J., Chai, T., Walsh, C.T. and Reimmann, C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front. Microbiol. 6 (2015) 170. [PMID: 25814981]
Accepted name: L-glutamate—[L-glutamyl-carrier protein] ligase
Reaction: ATP + L-glutamate + holo-[L-glutamyl-carrier protein] = AMP + diphosphate + L-glutamyl-[L-glutamyl-carrier protein] (overall reaction)
(1a) ATP + L-glutamate = diphosphate + (L-glutamyl)adenylate
(1b) (L-glutamyl)adenylate + holo-[L-glutamyl-carrier protein] = AMP + L-glutamyl-[L-glutamyl-carrier protein]
Other name(s): ambE (gene name)
Systematic name: L-glutamate:[L-glutamyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-glutamate to (L-glutamyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
References:
1. Rojas Murcia, N., Lee, X., Waridel, P., Maspoli, A., Imker, H.J., Chai, T., Walsh, C.T. and Reimmann, C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front. Microbiol. 6 (2015) 170. [PMID: 25814981]
Accepted name: phosphoribosylglycinamide formyltransferase 2
Reaction: ATP + formate + N1-(5-phospho-β-D-ribosyl)glycinamide = ADP + phosphate + N2-formyl-N1-(5-phospho-β-D-ribosyl)glycinamide
Other name(s): purT (gene name); GAR transformylase 2; GART2; glycinamide ribonucleotide transformylase 2; 5'-phosphoribosylglycinamide transformylase 2; GAR transformylase T
Systematic name: formate:N1-(5-phospho-β-D-ribosyl)glycinamide ligase (ADP-forming)
Comments: Two enzymes are known to catalyse the third step in de novo purine biosynthesis. This enzyme requires ATP and utilizes formate, which is provided by the hydrolysis of 10-formyltetrahydrofolate by EC 3.5.1.10, formyltetrahydrofolate deformylase. The other enzyme, EC 2.1.2.2, phosphoribosylglycinamide formyltransferase 1, utilizes 10-formyltetrahydrofolate directly. Formyl phosphate is formed during catalysis as an intermediate. The enzyme from the bacterium Escherichia coli can also catalyse the activity of EC 2.7.2.1, acetate kinase.
References:
1. Nagy, P.L., McCorkle, G.M. and Zalkin, H. purU, a source of formate for purT-dependent phosphoribosyl-N-formylglycinamide synthesis. J. Bacteriol. 175 (1993) 7066-7073. [PMID: 8226647]
2. Nygaard, P. and Smith, J.M. Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J. Bacteriol. 175 (1993) 3591-3597. [PMID: 8501063]
3. Marolewski, A., Smith, J.M. and Benkovic, S.J. Cloning and characterization of a new purine biosynthetic enzyme: a non-folate glycinamide ribonucleotide transformylase from E. coli. Biochemistry 33 (1994) 2531-2537. [PMID: 8117714]
4. Marolewski, A.E., Mattia, K.M., Warren, M.S. and Benkovic, S.J. Formyl phosphate: a proposed intermediate in the reaction catalyzed by Escherichia coli PurT GAR transformylase. Biochemistry 36 (1997) 6709-6716. [PMID: 9184151]
5. Thoden, J.B., Firestine, S., Nixon, A., Benkovic, S.J. and Holden, H.M. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Biochemistry 39 (2000) 8791-8802. [PMID: 10913290]
6. Jelsbak, L., Mortensen, M.IB., Kilstrup, M. and Olsen, J.E. The in vitro redundant enzymes PurN and PurT are both essential for systemic infection of mice in Salmonella enterica serovar Typhimurium. Infect. Immun. 84 (2016) 2076-2085. [PMID: 27113361]
Accepted name: 3-methyl-D-ornithine—L-lysine ligase
Reaction: ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + Pi + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
Glossary: L-pyrrolysine = N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
Other name(s): N6-[(2R,3R)-3-methylornithyl]-L-lysine synthase; 3-methylornithine—L-lysine ligase; pylC (gene name)
Systematic name: (3R)-3-methyl-D-ornithine:L-lysine γ-ligase (ADP-forming)
Comments: The enzyme participates in the biosynthesis of L-pyrrolysine, a naturally occurring, genetically coded amino acid found in some methanogenic archaea and a few bacterial species. L-pyrrolysine is present in several methyltransferases that are involved in methyl transfer from methylated amine compounds to coenzyme M.
References:
1. Gaston, M.A., Zhang, L., Green-Church, K.B. and Krzycki, J.A. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471 (2011) 647-650. [PMID: 21455182]
2. Cellitti, S.E., Ou, W., Chiu, H.P., Grunewald, J., Jones, D.H., Hao, X., Fan, Q., Quinn, L.L., Ng, K., Anfora, A.T., Lesley, S.A., Uno, T., Brock, A. and Geierstanger, B.H. D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine. Nat. Chem. Biol. 7 (2011) 528-530. [PMID: 21525873]
3. Quitterer, F., List, A., Beck, P., Bacher, A. and Groll, M. Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution. J. Mol. Biol. 424 (2012) 270-282. [PMID: 22985965]
Accepted name: glutamate—[amino group carrier protein] ligase
Reaction: ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate = ADP + phosphate + an [amino-group carrier protein]-C-terminal-γ-(L-glutamyl)-L-glutamate
Other name(s): argX (gene name)
Systematic name: L-glutamate:an [amino-group carrier protein]-C-terminal-L-glutamate ligase (ADP-forming)
Comments: The enzyme, originally characterized from the archaeon Sulfolobus acidocaldarius, is involved in L-arginine biosynthesis. The enzyme from the archaeon Thermococcus kodakarensis is bifunctional and also catalyses the activity of EC 6.3.2.43, [amino-group carrier protein]—L-2-aminoadipate ligase.
References:
1. Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277-283. [PMID: 23434852]
2. Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630-21643. [PMID: 27566549]
Accepted name: cytochrome-c oxidase
Reaction: 4 ferrocytochrome c + O2 + 8 H+[side 1] = 4 ferricytochrome c + 2 H2O + 4 H+[side 2]
Other name(s): cytochrome aa3; cytochrome caa3; cytochrome bb3; cytochrome cbb3; cytochrome ba3; cytochrome a3; Warburg's respiratory enzyme; indophenol oxidase; indophenolase; complex IV (mitochondrial electron transport); ferrocytochrome c oxidase; cytochrome oxidase (ambiguous); NADH cytochrome c oxidase (incorrect)
Systematic name: ferrocytochrome-c:oxygen oxidoreductase
Comments: An oligomeric membrane heme-Cu:O2 reductase-type enzyme that terminates the respiratory chains of aerobic and facultative aerobic organisms. The reduction of O2 to water is accompanied by the extrusion of four protons. The cytochrome-aa3 enzymes of mitochondria and many bacterial species are the most abundant group, but other variations, such as the bacterial cytochrome-cbb3 enzymes, also exist. All of the variants have a conserved catalytic core subunit (subunit I) that contains a low-spin heme (of a- or b-type), a binuclear metal centre composed of a high-spin heme iron (of a-, o-, or b-type heme, referred to as a3, o3 or b3 heme), and a Cu atom (CuB). Besides subunit I, the enzyme usually has at least two other core subunits: subunit II is the primary electron acceptor; subunit III usually does not contain any cofactors, but in the case of cbb3-type enzymes it is a diheme c-type cytochrome. While most bacterial enzymes consist of only 3-4 subunits, the mitochondrial enzyme is much more complex and contains 14 subunits.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-16-5
References:
1. Keilin, D. and Hartree, E.F. Cytochrome oxidase. Proc. R. Soc. Lond. B Biol. Sci. 125 (1938) 171-186.
2. Keilin, D. and Hartree, E.F. Cytochrome and cytochrome oxidase. Proc. R. Soc. Lond. B Biol. Sci. 127 (1939) 167-191.
3. Wainio, W.W., Eichel, B. and Gould, A. Ion and pH optimum for the oxidation of ferrocytochrome c by cytochrome c oxidase in air. J. Biol. Chem. 235 (1960) 1521-1525.
4. Yonetani, T. Studies on cytochrome oxidase. II. Steady state properties. J. Biol. Chem. 235 (1960) 3138-3243. [PMID: 13787372]
5. Yonetani, T. Studies on cytochrome oxidase. III. Improved purification and some properties. J. Biol. Chem. 236 (1961) 1680-1688. [PMID: 13787373]
6. Henning, W., Vo, L., Albanese, J. and Hill, B.C. High-yield purification of cytochrome aa3 and cytochrome caa3 oxidases from Bacillus subtilis plasma membranes. Biochem. J. 309 (1995) 279-283. [PMID: 7619069]
7. Keightley, J.A., Zimmermann, B.H., Mather, M.W., Springer, P., Pastuszyn, A., Lawrence, D.M. and Fee, J.A. Molecular genetic and protein chemical characterization of the cytochrome ba3 from Thermus thermophilus HB8. J. Biol. Chem. 270 (1995) 20345-20358. [PMID: 7657607]
8. Ducluzeau, A.L., Ouchane, S. and Nitschke, W. The cbb3 oxidases are an ancient innovation of the domain bacteria. Mol. Biol. Evol. 25 (2008) 1158-1166. [PMID: 18353797]
Accepted name: ferredoxin—quinone oxidoreductase (H+-translocating)
Reaction: 2 reduced ferredoxin [iron-sulfur] cluster + plastoquinone + 6 H+[side 1] = 2 oxidized ferredoxin [iron-sulfur] cluster + plastoquinol + 7 H+[side 2]
Other name(s): NDH-1L complex; NDH-1L' complex; NDH11 complex; NDH12 complex
Systematic name: ferredoxin:quinone oxidoreductase (H+-translocating)
Comments: The enzyme, present in plants and cyanobacteria, couples electron transport from ferredoxin to plastoquinone and proton pumping from the cytoplasm to the thylakoid lumen. It participates in cyclic electron flow, retuning electrons generated by photosystem I to the plastoquinone pool, thus bypassing the generation of reducing power. It may also participate in respiration using electrons originating from NADPH via the action of EC 1.18.1.2, ferredoxin—NADP+ reductase (FNR) operating in the direction of ferredoxin reduction. It is a large complex, with some of its subunits resembling those from the bacterial/mitochondrial EC 7.1.1.2, NADH:ubiquinone reductase (H+-translocating). However, it lacks the NADH-oxidizing module and instead has a module that interacts with ferredoxin. Several forms of the enzyme exist, differing in their exact combination of subunits used. Some of the forms participate in carbon dioxide hydration rather than electron transfer.
References:
1. Arteni, A.A., Zhang, P., Battchikova, N., Ogawa, T., Aro, E.M. and Boekema, E.J. Structural characterization of NDH-1 complexes of Thermosynechococcus elongatus by single particle electron microscopy. Biochim. Biophys. Acta 1757 (2006) 1469-1475. [PMID: 16844076]
2. Battchikova, N., Wei, L., Du, L., Bersanini, L., Aro, E.M. and Ma, W. Identification of novel Ssl0352 protein (NdhS), essential for efficient operation of cyclic electron transport around photosystem I, in NADPH:plastoquinone oxidoreductase (NDH-1) complexes of Synechocystis sp. PCC 6803. J. Biol. Chem. 286 (2011) 36992-37001. [PMID: 21880717]
3. Yamamoto, H. and Shikanai, T. In planta mutagenesis of Src homology 3 domain-like fold of NdhS, a ferredoxin-binding subunit of the chloroplast NADH dehydrogenase-like complex in Arabidopsis: a conserved Arg-193 plays a critical role in ferredoxin binding. J. Biol. Chem. 288 (2013) 36328-36337. [PMID: 24225949]
4. Ma, W. and Ogawa, T. Oxygenic photosynthesis-specific subunits of cyanobacterial NADPH dehydrogenases. IUBMB Life 67 (2015) 3-8. [PMID: 25564967]
5. Peltier, G., Aro, E.M. and Shikanai, T. NDH-1 and NDH-2 plastoquinone reductases in oxygenic photosynthesis. Annu. Rev. Plant Biol. 67 (2016) 55-80. [PMID: 26735062]
6. Laughlin, T.G., Bayne, A.N., Trempe, J.F., Savage, D.F. and Davies, K.M. Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature 566 (2019) 411-414. [PMID: 30742075]
7. Schuller, J.M., Birrell, J.A., Tanaka, H., Konuma, T., Wulfhorst, H., Cox, N., Schuller, S.K., Thiemann, J., Lubitz, W., Setif, P., Ikegami, T., Engel, B.D., Kurisu, G. and Nowaczyk, M.M. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science 363 (2019) 257-260. [PMID: 30573545]
8. Zhang, C., Shuai, J., Ran, Z., Zhao, J., Wu, Z., Liao, R., Wu, J., Ma, W. and Lei, M. Structural insights into NDH-1 mediated cyclic electron transfer. Nat. Commun. 11 (2020) 888. [PMID: 32060291]
Accepted name: P-type Mn2+ transporter
Reaction: ATP + H2O + Mn2+[side 1] = ADP + phosphate + Mn2+[side 2]
Other name(s): Mn(II)-translocating P-type ATPase; Mn2+-exporting ATPase; P1B-type ATPase (ambiguous); ctpC (gene name)
Systematic name: ATP phosphohydrolase (P-type, Mn2+-exporting)
Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. The enzyme, detected in mycobacteria, is a high affinity slow turnover ATPase exporting Mn2+.
References:
1. Padilla-Benavides, T., Long, J.E., Raimunda, D., Sassetti, C.M. and Arguello, J.M. A novel P(1B)-type Mn2+-transporting ATPase is required for secreted protein metallation in mycobacteria. J. Biol. Chem. 288 (2013) 11334-11347. [PMID: 23482562]
Accepted name: ABC-type antigen peptide transporter
Reaction: ATP + H2O + antigen peptide[side 1] = ADP + phosphate + antigen peptide[side 2]
Other name(s): TAP1 (gene name); TAP2 (gene name)
Systematic name: ATP phosphohydrolase (ABC-type, antigen peptide-exporting)
Comments: An ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. Does not undergo phosphorylation during the transport process. This entry describes vertebrate transporters involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum for association with major histocompatibility complex (MHC) class I molecules. The substrates are generated mainly from degradation of cytosolic proteins by the proteasome.
References:
1. Bahram, S., Arnold, D., Bresnahan, M., Strominger, J.L. and Spies, T. Two putative subunits of a peptide pump encoded in the human major histocompatibility complex class II region. Proc. Natl. Acad. Sci. USA 88 (1991) 10094-10098. [PMID: 1946428]
2. Momburg, F., Roelse, J., Howard, J.C., Butcher, G.W., Hammerling, G.J. and Neefjes, J.J. Selectivity of MHC-encoded peptide transporters from human, mouse and rat. Nature 367 (1994) 648-651. [PMID: 8107849]
3. Nijenhuis, M. and Hammerling, G.J. Multiple regions of the transporter associated with antigen processing (TAP) contribute to its peptide binding site. J. Immunol. 157 (1996) 5467-5477. [PMID: 8955196]