An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: hydroxylamine dehydrogenase
Reaction: hydroxylamine + H2O + 4 ferricytochrome c = nitrite + 4 ferrocytochrome c + 5 H+
Other name(s): HAO (ambiguous); hydroxylamine oxidoreductase (ambiguous); hydroxylamine oxidase (misleading)
Systematic name: hydroxylamine:ferricytochrome-c oxidoreductase (nitrite-forming)
Comments: The enzymes from the nitrifying bacterium Nitrosomonas europaea [1,4] and the methylotrophic bacterium Methylococcus capsulatus [5] are hemoproteins with seven c-type hemes and one specialized P-460-type heme per subunit. The enzyme converts hydroxylamine to nitrite via an enzyme-bound nitroxyl intermediate [3]. While nitrite is the main product, the enzyme from Nitrosomonas europaea can also produce nitric oxide by catalysing the activity of EC 1.7.2.9, hydroxylamine oxidase [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-43-8
References:
1. Rees, M. Studies of the hydroxylamine metabolism of Nitrosomonas europaea. I. Purification of hydroxylamine oxidase. Biochemistry 7 (1968) 353-366. [PMID: 5758552]
2. Hooper, A.B. and Terry, K.R. Hydroxylamine oxidoreductase of Nitrosomonas. Production of nitric oxide from hydroxylamine. Biochim. Biophys. Acta 571 (1979) 12-20. [PMID: 497235]
3. Hooper, A.B. and Balny, C. Reaction of oxygen with hydroxylamine oxidoreductase of Nitrosomonas: fast kinetics. FEBS Lett. 144 (1982) 299-303. [PMID: 7117545]
4. Lipscomb, J.D. and Hooper, A.B. Resolution of multiple heme centers of hydroxylamine oxidoreductase from Nitrosomonas. 1. Electron paramagnetic resonance spectroscopy. Biochemistry 21 (1982) 3965-3972. [PMID: 6289867]
5. Poret-Peterson, A.T., Graham, J.E., Gulledge, J. and Klotz, M.G. Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath. ISME J. 2 (2008) 1213-1220. [PMID: 18650926]
Accepted name: hydrazine synthase
Reaction: hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c
Glossary: nitric oxide = nitrogen monoxide = NO
Other name(s): HZS
Systematic name: hydrazine:ferricytochrome-c oxidoreductase
Comments: The enzyme, characterized from anaerobic ammonia oxidizers (anammox bacteria), is one of only a few enzymes that are known to form an N-N bond (other examples include EC 1.7.1.14, nitric oxide reductase [NAD(P)+, nitrous oxide-forming] and EC 4.8.1.1, L-piperazate synthase). The enzyme from the bacterium Candidatus Kuenenia stuttgartiensis is a dimer of heterotrimers and contains multiple c-type cytochromes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kartal, B., Maalcke, W.J., de Almeida, N.M., Cirpus, I., Gloerich, J., Geerts, W., Op den Camp, H.J., Harhangi, H.R., Janssen-Megens, E.M., Francoijs, K.J., Stunnenberg, H.G., Keltjens, J.T., Jetten, M.S. and Strous, M. Molecular mechanism of anaerobic ammonium oxidation. Nature 479 (2011) 127-130. [PMID: 21964329]
2. Dietl, A., Ferousi, C., Maalcke, W.J., Menzel, A., de Vries, S., Keltjens, J.T., Jetten, M.S., Kartal, B. and Barends, T.R. The inner workings of the hydrazine synthase multiprotein complex. Nature 527 (2015) 394-397. [PMID: 26479033]
Accepted name: hydroxylamine oxidase
Reaction: hydroxylamine + 3 ferricytochrome c = nitric oxide + 3 ferrocytochrome c + 3 H+
Other name(s): HOX
Systematic name: hydroxylamine:ferricytochrome-c oxidoreductase (nitric acid-forming)
Comments: The enzyme, characterized from the anaerobic ammonium-oxidizing (anammox) bacterium Kuenenia stuttgartiensis, is very similar to EC 1.7.2.6, hydroxylamine dehydrogenase. Both enzymes are homotrimeric enzymes in which each subunit contains seven c-type hemes and one specialized P460-type heme that is bound to a tyrosine residue in an adjacent subunit. However, this enzyme catalyses only the 3 electron oxidation of hydroxylamine, forming nitric oxide, and is not capable of performing further oxidation to form nitrite.
References:
1. Maalcke, W.J., Dietl, A., Marritt, S.J., Butt, J.N., Jetten, M.S., Keltjens, J.T., Barends, T.R. and Kartal, B. Structural basis of biological NO generation by octaheme oxidoreductases. J. Biol. Chem. 289 (2014) 1228-1242. [PMID: 24302732]
Accepted name: L-aspartate N-monooxygenase (nitrosuccinate-forming)
Reaction: L-aspartate + 3 NADPH + 3 H+ + 3 O2 = (2S)- 2-nitrobutanedioate + 3 NADP+ + 4 H2O
(1a) L-aspartate + NADPH + H+ + O2 = N-hydroxy-L-aspartate + NADP+ + H2O
(1b) N-hydroxy-L-aspartate + NADPH + H+ + O2 = N,N-dihydroxy-L-aspartate + NADP+ + H2O
(1c) N,N-dihydroxy-L-aspartate = (2S)-2-nitrosobutanedioate + H2O (spontaneous)
(1d) (2S)-2-nitrosobutanedioate + NADPH + H+ + O2 = (2S)-2-nitrobutanedioate + NADP+ + H2O
Glossary: 2-nitrobutanedioate = nitrosuccinate
Other name(s): creE (gene name)
Systematic name: L-aspartate,NADPH:oxygen oxidoreductase [(2S)-2-nitrobutanedioate-forming]
Comments: The enzyme, found in some Actinobacteria, is involved in a pathway that forms nitrite, which is subsequently used to generate a diazo group in some secondary metabolites. Requires an FAD cofactor.
References:
1. Sugai, Y., Katsuyama, Y. and Ohnishi, Y. A nitrous acid biosynthetic pathway for diazo group formation in bacteria. Nat. Chem. Biol. 12 (2016) 73-75. [PMID: 26689788]
2. Hagihara, R., Katsuyama, Y., Sugai, Y., Onaka, H. and Ohnishi, Y. Novel desferrioxamine derivatives synthesized using the secondary metabolism-specific nitrous acid biosynthetic pathway in Streptomyces davawensis, J. Antibiot. (Tokyo) 71 (2018) 911-919. [PMID: 30120394]
Accepted name: 3-amino-4-hydroxybenzoate 2-monooxygenase
Reaction: 3-amino-4-hydroxybenzoate + NADPH + H+ + O2 = 3-amino-2,4-dihydroxybenzoate + NADP+ + H2O
For diagram of reaction, click here
Other name(s): creL (gene name); ptmB3 (gene name); ptnB3 (gene name)
Systematic name: 3-amino-4-hydroxybenzoate,NADPH:oxygen oxidoreductase (2-hydroxylating)
Comments: Requires FAD. The CreL enzyme from the bacterium Streptomyces cremeus participates in the biosynthesis of cremeomycin. The PrmB3 and PtnB3 enzymes from Streptomyces platensis are involved in the biosynthesis of platensimycin and platencin, respectively.
References:
1. Smanski, M.J., Yu, Z., Casper, J., Lin, S., Peterson, R.M., Chen, Y., Wendt-Pienkowski, E., Rajski, S.R. and Shen, B. Dedicated ent-kaurene and ent-atiserene synthases for platensimycin and platencin biosynthesis. Proc. Natl. Acad. Sci. USA 108 (2011) 13498-13503. [PMID: 21825154]
2. Waldman, A.J., Pechersky, Y., Wang, P., Wang, J.X. and Balskus, E.P. The cremeomycin biosynthetic gene cluster encodes a pathway for diazo formation. Chembiochem 16 (2015) 2172-2175. [PMID: 26278892]
3. Sugai, Y., Katsuyama, Y. and Ohnishi, Y. A nitrous acid biosynthetic pathway for diazo group formation in bacteria. Nat. Chem. Biol. 12 (2016) 73-75. [PMID: 26689788]
4. Dong, L.B., Rudolf, J.D., Kang, D., Wang, N., He, C.Q., Deng, Y., Huang, Y., Houk, K.N., Duan, Y. and Shen, B. Biosynthesis of thiocarboxylic acid-containing natural products. Nat. Commun. 9 (2018) 2362. [PMID: 29915173]
Accepted name: nitrosourea synthase
Reaction: Nω-methyl-L-arginine + 2 NADH + H+ + 3 O2 = Nδ-hydroxy-Nω-methyl-Nω-nitroso-L-citrulline + 2 NAD+ + 3 H2O (overall reaction)
(1a) Nω-methyl-L-arginine + NADH + H+ + O2 = Nδ-hydroxy-Nω-methyl-L-arginine + NAD+ + H2O
(1b) Nδ-hydroxy-Nω-methyl-L-arginine + NADH + H+ + O2 = Nδ,Nω;-dihydroxy-Nω-methyl-L-arginine + NAD+ + H2O
(1c) Nδ,Nω;-dihydroxy-Nω-methyl-L-arginine + O2 = Nδ-hydroxy-Nω-methyl-Nω-nitroso-L-citrulline + H2O
Other name(s): sznF (gene name); StzF
Systematic name: Nω-methyl-L-arginine,NADH:oxygen oxidoreductase (Nδ-hydroxy-Nω-methyl-Nω-nitroso-L-citrulline-forming)
Comments: The enzyme, characterized from the bacterium Streptomyces achromogenes subsp. streptozoticus, catalyses a complex multi-step reaction during the biosynthesis of the glucosamine-nitrosourea antibiotic streptozotocin. The overall reaction is an oxidative rearrangement of the guanidine group of Nω-methyl-L-arginine, generating an N-nitrosourea product. The enzyme hydroxylates its substrate at the Nδ position, followed by a second hydroxylation at the Nω' position. It then catalyses an oxidative rearrangement to form Nδ-hydroxy-Nω-methyl-Nω-nitroso-L-citrulline. This product is unstable, and degrades non-enzymically into nitric oxide and the denitrosated product Nδ-hydroxy-Nω-methyl-L-citrulline. The enzyme contains two active sites, each of which utilizes a different iron-containing cofactor.
References:
1. Ng, T.L., Rohac, R., Mitchell, A.J., Boal, A.K. and Balskus, E.P. An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. Nature 566 (2019) 94-99. [PMID: 30728519]
2. He, H.Y., Henderson, A.C., Du, Y.L. and Ryan, K.S. Two-enzyme pathway links l-arginine to nitric oxide in N-nitroso biosynthesis. J. Am. Chem. Soc. 141 (2019) 4026-4033. [PMID: 30763082]
3. McBride, M.J., Sil, D., Ng, T.L., Crooke, A.M., Kenney, G.E., Tysoe, C.R., Zhang, B., Balskus, E.P., Boal, A.K., Krebs, C. and Bollinger, J.M., Jr. A peroxodiiron(III/III) intermediate mediating both N-hydroxylation steps in biosynthesis of the N-nitrosourea pharmacophore of streptozotocin by the multi-domain metalloenzyme SznF. J. Am. Chem. Soc. 142 (2020) 11818-11828. [PMID: 32511919]
4. McBride, M.J., Pope, S.R., Hu, K., Okafor, C.D., Balskus, E.P., Bollinger, J.M., Jr. and Boal, A.K. Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N-nitrosourea-producing enzyme SznF. Proc. Natl. Acad. Sci. USA 118 (2021) . [PMID: 33468680]
5. Wang, J., Wang, X., Ouyang, Q., Liu, W., Shan, J., Tan, H., Li, X. and Chen, G. N-nitrosation mechanism catalyzed by non-heme iron-containing enzyme SznF involving intramolecular oxidative rearrangement. Inorg. Chem. 60 (2021) 7719-7731. [PMID: 34004115]
[EC 1.16.1.4 Deleted entry: cob(II)alamin reductase. This entry has been deleted since no specific enzyme catalysing this activity has been identified and it has been shown that cob(II)alamin is efficiently reduced by free dihydroflavins and by non-specific reduced flavoproteins (EC 1.16.1.4 created 1972 as EC 1.6.99.9, transferred 2002 to EC 1.16.1.4, deleted 2021)]
Accepted name: cuproxidase
Reaction: 4 Cu+ + 4 H+ + O2 = 4 Cu2+ + 2 H2O
Other name(s): cueO (gene name); cuprous oxidase; Cu(I) oxidase; copper efflux oxidase
Systematic name: copper(I):oxygen oxidoreductase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in copper tolerance under aerobic conditions. The enzyme contains a substrate binding (type 1) copper site and a trinuclear copper center (consisting of type 2 and type 3 copper sites) in which oxygen binding and reduction takes place. It also contains a methionine rich region that can bind additional copper ions. In vitro, if the substrate binding site is occupied by copper(II), the enzyme can function as a laccase-type quinol oxidase (EC 1.10.3.2) . However, in vivo this site is occupied by a copper(I) ion and the enzyme functions as a cuprous oxidase.
References:
1. Kim, C., Lorenz, W.W., Hoopes, J.T. and Dean, J.F. Oxidation of phenolate siderophores by the multicopper oxidase encoded by the Escherichia coli yacK gene. J. Bacteriol. 183 (2001) 4866-4875. [PMID: 11466290]
2. Grass, G. and Rensing, C. CueO is a multi-copper oxidase that confers copper tolerance in Escherichia coli, Biochem. Biophys. Res. Commun. 286 (2001) 902-908. [PMID: 11527384]
3. Outten, F.W., Huffman, D.L., Hale, J.A. and O'Halloran, T.V. The independent cue and cus systems confer copper tolerance during aerobic and anaerobic growth in Escherichia coli, J. Biol. Chem. 276 (2001) 30670-30677. [PMID: 11399769]
4. Roberts, S.A., Weichsel, A., Grass, G., Thakali, K., Hazzard, J.T., Tollin, G., Rensing, C. and Montfort, W.R. Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in Escherichia coli, Proc. Natl. Acad. Sci. USA 99 (2002) 2766-2771. [PMID: 11867755]
5. Roberts, S.A., Wildner, G.F., Grass, G., Weichsel, A., Ambrus, A., Rensing, C. and Montfort, W.R. A labile regulatory copper ion lies near the T1 copper site in the multicopper oxidase CueO. J. Biol. Chem. 278 (2003) 31958-31963. [PMID: 12794077]
6. Singh, S.K., Grass, G., Rensing, C. and Montfort, W.R. Cuprous oxidase activity of CueO from Escherichia coli, J. Bacteriol. 186 (2004) 7815-7817. [PMID: 15516598]
7. Galli, I., Musci, G. and Bonaccorsi di Patti, M.C. Sequential reconstitution of copper sites in the multicopper oxidase CueO. J. Biol. Inorg. Chem. 9 (2004) 90-95. [PMID: 14648285]
8. Djoko, K.Y., Chong, L.X., Wedd, A.G. and Xiao, Z. Reaction mechanisms of the multicopper oxidase CueO from Escherichia coli support its functional role as a cuprous oxidase. J. Am. Chem. Soc. 132 (2010) 2005-2015. [PMID: 20088522]
9. Singh, S.K., Roberts, S.A., McDevitt, S.F., Weichsel, A., Wildner, G.F., Grass, G.B., Rensing, C. and Montfort, W.R. Crystal structures of multicopper oxidase CueO bound to copper(I) and silver(I): functional role of a methionine-rich sequence. J. Biol. Chem. 286 (2011) 37849-37857. [PMID: 21903583]
10. Cortes, L., Wedd, A.G. and Xiao, Z. The functional roles of the three copper sites associated with the methionine-rich insert in the multicopper oxidase CueO from E. coli, Metallomics 7 (2015) 776-785. [PMID: 25679350]
Accepted name: arsenite methyltransferase
Reaction: (1) S-adenosyl-L-methionine + arsenic triglutathione + thioredoxin + 2 H2O = S-adenosyl-L-homocysteine + methylarsonous acid + 3 glutathione + thioredoxin disulfide
(2) 2 S-adenosyl-L-methionine + arsenic triglutathione + 2 thioredoxin + H2O = S-adenosyl-L-homocysteine + dimethylarsinous acid + 3 glutathione + 2 thioredoxin disulfide
(3) 3 S-adenosyl-L-methionine + arsenic triglutathione + 3 thioredoxin = S-adenosyl-L-homocysteine + trimethylarsane + 3 glutathione + 3 thioredoxin disulfide
For diagram of rection click here
Other name(s): AS3MT (gene name); arsM (gene name); S-adenosyl-L-methionine:arsenic(III) methyltransferase; S-adenosyl-L-methionine:methylarsonite As-methyltransferase; methylarsonite methyltransferase
Systematic name: S-adenosyl-L-methionine:arsenous acid As-methyltransferase
Comments: An enzyme responsible for synthesis of trivalent methylarsenical antibiotics in microbes [11] or detoxification of inorganic arsenous acid in animals. The in vivo substrate is arsenic triglutathione or similar thiol (depending on the organism) [6], from which the arsenic is transferred to the enzyme forming bonds with the thiol groups of three cysteine residues [10] via a disulfide bond cascade pathway [7, 8]. Most of the substrates undergo two methylations and are converted to dimethylarsinous acid [9]. However, a small fraction are released earlier as methylarsonous acid, and a smaller amount proceeds via a third methylation, resulting in the volatile product trimethylarsane. Methylation involves temporary oxidation to arsenic(V) valency, followed by reduction back to arsenic(III) valency using electrons provided by thioredoxin or a similar reduction system. The arsenic(III) products are quickly oxidized in the presence of oxygen to the corresponding arsenic(V) species.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 167140-41-2
References:
1. Zakharyan, R.A., Wu, Y., Bogdan, G.M. and Aposhian, H.V. Enzymatic methylation of arsenic compounds: assay, partial purification, and properties of arsenite methyltransferase and monomethylarsonic acid methyltransferase of rabbit liver. Chem. Res. Toxicol. 8 (1995) 1029-1038. [PMID: 8605285]
2. Zakharyan, R.A., Wildfang, E. and Aposhian, H.V. Enzymatic methylation of arsenic compounds. III. The marmoset and tamarin, but not the rhesus, monkeys are deficient in methyltransferases that methylate inorganic arsenic. Toxicol. Appl. Pharmacol. 140 (1996) 77-84. [PMID: 8806872]
3. Zakharyan, R.A. and Aposhian, H.V. Enzymatic reduction of arsenic compounds in mammalian systems: the rate-limiting enzyme of rabbit liver arsenic biotransformation is MMA(V) reductase. Chem. Res. Toxicol. 12 (1999) 1278-1283. [PMID: 10604879]
4. Zakharyan, R.A., Ayala-Fierro, F., Cullen, W.R., Carter, D.M. and Aposhian, H.V. Enzymatic methylation of arsenic compounds. VII. Monomethylarsonous acid (MMAIII) is the substrate for MMA methyltransferase of rabbit liver and human hepatocytes. Toxicol. Appl. Pharmacol. 158 (1999) 9-15. [PMID: 10387927]
5. Lin, S., Shi, Q., Nix, F.B., Styblo, M., Beck, M.A., Herbin-Davis, K.M., Hall, L.L., Simeonsson, J.B. and Thomas, D.J. A novel S-adenosyl-L-methionine:arsenic(III) methyltransferase from rat liver cytosol. J. Biol. Chem. 277 (2002) 10795-10803. [PMID: 11790780]
6. Hayakawa, T., Kobayashi, Y., Cui, X. and Hirano, S. A new metabolic pathway of arsenite: arsenic-glutathione complexes are substrates for human arsenic methyltransferase Cyt19. Arch Toxicol 79 (2005) 183-191. [PMID: 15526190]
7. Dheeman, D.S., Packianathan, C., Pillai, J.K. and Rosen, B.P. Pathway of human AS3MT arsenic methylation. Chem. Res. Toxicol. 27 (2014) 1979-1989. [PMID: 25325836]
8. Marapakala, K., Packianathan, C., Ajees, A.A., Dheeman, D.S., Sankaran, B., Kandavelu, P. and Rosen, B.P. A disulfide-bond cascade mechanism for arsenic(III) S-adenosylmethionine methyltransferase. Acta Crystallogr. D Biol. Crystallogr. 71 (2015) 505-515. [PMID: 25760600]
9. Yang, H.C. and Rosen, B.P. New mechanisms of bacterial arsenic resistance. Biomed J 39 (2016) 5-13. [PMID: 27105594]
10. Packianathan, C., Kandavelu, P. and Rosen, B.P. The structure of an As(III) S-adenosylmethionine methyltransferase with 3-coordinately bound As(III) depicts the first step in catalysis. Biochemistry 57 (2018) 4083-4092. [PMID: 29894638]
11. Chen, J., Yoshinaga, M. and Rosen, B.P. The antibiotic action of methylarsenite is an emergent property of microbial communities. Mol. Microbiol. 111 (2019) 487-494. [PMID: 30520200]
Accepted name: 3-amino-4-hydroxybenzoate 4-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-amino-2,4-dihydroxybenzoate = S-adenosyl-L-homocysteine + 3-amino-2-hydroxy-4-methoxybenzoate
For diagram of reaction, click here
Glossary: cremeomycin = 6-carboxy-2-diazonio-3-methoxyphenolate
Other name(s): creN (gene name)
Systematic name: S-adenosyl-L-methionine:3-amino-4-hydroxybenzoate 4-O-methyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces cremeus, is involved in cremeomycin biosynthesis.
References:
1. Waldman, A.J., Pechersky, Y., Wang, P., Wang, J.X. and Balskus, E.P. The cremeomycin biosynthetic gene cluster encodes a pathway for diazo formation. Chembiochem 16 (2015) 2172-2175. [PMID: 26278892]
Accepted name: arginine Nω-methyltransferase
Reaction: S-adenosyl-L-methionine + L-arginine = S-adenosyl-L-homocysteine + Nω-methyl-L-arginine
Other name(s): sznE (gene name); stzE (gene name)
Systematic name: S-adenosyl-L-methionine:L-arginine Nω-methyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces achromogenes subsp. streptozoticus, participates in the biosynthesis of the glucosamine-nitrosourea antibiotic streptozotocin.
References:
1. Ng, T.L., Rohac, R., Mitchell, A.J., Boal, A.K. and Balskus, E.P. An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. Nature 566 (2019) 94-99. [PMID: 30728519]
2. He, H.Y., Henderson, A.C., Du, Y.L. and Ryan, K.S. Two-enzyme pathway links l-arginine to nitric oxide in N-nitroso biosynthesis. J. Am. Chem. Soc. 141 (2019) 4026-4033. [PMID: 30763082]
Accepted name: L-carnitine—corrinoid protein Co-methyltransferase
Reaction: L-carnitine + a [Co(I) quaternary-amine-specifc corrinoid protein] = a [methyl-Co(III) quaternary-amine-specific corrinoid protein] + L-norcarnitine
Glossary: L-norcarnitine = (3R)-4-(dimethylamino)-3-hydroxybutanoate
Other name(s): mtcB (gene name)
Systematic name: L-carnitine:[Co(I) quaternary-amine-specifc corrinoid protein] Co-methyltransferase
Comments: The enzyme, characterized from the bacterium Eubacterium limosum, is a component of a system that transfers a methyl group from L-carnitine to tetrahydrofolate, as part of an L-carnitine degradation pathway. The resulting 5-methyltetrahydrofolate is processed to acetyl-CoA via the Wood—Ljungdahl pathway.
References:
1. Kountz, D.J., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase. J. Biol. Chem. 295 (2020) 11971-11981. [PMID: 32571881]
Accepted name: ureidoglycine carbamoyltransferase
Reaction: carbamoyl phosphate + (S)-(carbamoylamino)glycine = phosphate + allantoate
Other name(s): UGTCase
Systematic name: carbamoyl phosphate:(S)-(carbamoylamino)glycine carbamoyltransferase
Comments: The enzyme, characterized from the bacterium Rubrobacter xylanophilus, is involved in a purine degradation pathway.
References:
1. Barba, M., Dutoit, R., Legrain, C. and Labedan, B. Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism. BMC Syst Biol 7 (2013) 99. [PMID: 24093154]
Accepted name: α-tubulin N-acetyltransferase
Reaction: acetyl-CoA + [α-tubulin]-L-lysine = CoA + [α-tubulin]-N6-acetyl-L-lysine
Other name(s): ATAT1 (gene name); MEC17 (gene name); α-tubulin acetylase; TAT; α-tubulin acetyltransferase; tubulin N-acetyltransferase (ambiguous); acetyl-CoA:α-tubulin-L-lysine N-acetyltransferase; acetyl-CoA:[α-tubulin]-L-lysine 6-N-acetyltransferase
Systematic name: acetyl-CoA:[α-tubulin]-L-lysine N6-acetyltransferase
Comments: The enzyme is conserved from protists to mammals and is present in flowering plants. In most organisms it acetylates L-lysine at position 40 of α-tubulin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 99889-90-4
References:
1. Greer, K., Maruta, H., L'Hernault, S.W. and Rosenbaum, J.L. α-Tubulin acetylase activity in isolated Chlamydomonas flagella. J. Cell Biol. 101 (1985) 2081-2084. [PMID: 4066751]
2. Akella, J.S., Wloga, D., Kim, J., Starostina, N.G., Lyons-Abbott, S., Morrissette, N.S., Dougan, S.T., Kipreos, E.T. and Gaertig, J. MEC-17 is an α-tubulin acetyltransferase. Nature 467 (2010) 218-222. [PMID: 20829795]
3. Shida, T., Cueva, J.G., Xu, Z., Goodman, M.B. and Nachury, M.V. The major α-tubulin K40 acetyltransferase αTAT1 promotes rapid ciliogenesis and efficient mechanosensation. Proc. Natl. Acad. Sci. USA 107 (2010) 21517-21522. [PMID: 21068373]
4. Taschner, M., Vetter, M. and Lorentzen, E. Atomic resolution structure of human α-tubulin acetyltransferase bound to acetyl-CoA. Proc. Natl. Acad. Sci. USA 109 (2012) 19649-19654. [PMID: 23071318]
5. Friedmann, D.R., Aguilar, A., Fan, J., Nachury, M.V. and Marmorstein, R. Structure of the α-tubulin acetyltransferase, αTAT1, and implications for tubulin-specific acetylation. Proc. Natl. Acad. Sci. USA 109 (2012) 19655-19660. [PMID: 23071314]
6. Kalebic, N., Sorrentino, S., Perlas, E., Bolasco, G., Martinez, C. and Heppenstall, P.A. αTAT1 is the major α-tubulin acetyltransferase in mice. Nat. Commun. 4 (2013) 1962. [PMID: 23748901]
Accepted name: acyl-[acyl-carrier-protein]—UDP-N-acetylglucosamine O-acyltransferase
Reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + UDP-N-acetyl-α-D-glucosamine = an [acyl-carrier protein] + a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-α-D-glucosamine
For diagram of reaction click here
Other name(s): lpxA (gene name); UDP-N-acetylglucosamine acyltransferase; uridine diphosphoacetylglucosamine acyltransferase; acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase; (R)-3-hydroxytetradecanoyl-[acyl-carrier-protein]:UDP-N-acetylglucosamine 3-O-(3-hydroxytetradecanoyl)transferase
Systematic name: (3R)-3-hydroxyacyl-[acyl-carrier protein]:UDP-N-acetyl-α-D-glucosamine 3-O-(3-hydroxyacyl)transferase
Comments: Involved with EC 2.4.1.182, lipid-A-disaccharide synthase, and EC 2.7.1.130, tetraacyldisaccharide 4'-kinase, in the biosynthesis of the phosphorylated glycolipid, Lipid A, in the outer membrane of Gram-negative bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 105843-69-4
References:
1. Anderson, M.S., Bulawa, C.E. and Raetz, C.R.H. The biosynthesis of gram-negative endotoxin. Formation of lipid A precursors from UDP-GlcNAc in extracts of Escherichia coli, J. Biol. Chem. 260 (1985) 15536-15541. [PMID: 3905795]
2. Anderson, M.S., Bull, H.G., Galloway, S.M., Kelly, T.M., Mohan, S., Radika, K. and Raetz, C.R. UDP-N-acetylglucosamine acyltransferase of Escherichia coli. The first step of endotoxin biosynthesis is thermodynamically unfavorable. J. Biol. Chem. 268 (1993) 19858-19865. [PMID: 8366124]
3. Raetz, C.R. and Roderick, S.L. A left-handed parallel β helix in the structure of UDP-N-acetylglucosamine acyltransferase. Science 270 (1995) 997-1000. [PMID: 7481807]
4. Williams, A.H. and Raetz, C.R. Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase. Proc. Natl. Acad. Sci. USA 104 (2007) 13543-13550. [PMID: 17698807]
5. Bainbridge, B.W., Karimi-Naser, L., Reife, R., Blethen, F., Ernst, R.K. and Darveau, R.P. Acyl chain specificity of the acyltransferases LpxA and LpxD and substrate availability contribute to lipid A fatty acid heterogeneity in Porphyromonas gingivalis, J. Bacteriol. 190 (2008) 4549-4558. [PMID: 18456814]
[EC 2.3.1.182 Transferred entry: (R)-citramalate synthase. Now classified as EC 2.3.3.21, (R)-citramalate synthase. (EC 2.3.1.182 created 2007, deleted 2021)]
Accepted name: Kdo2-lipid IVA acyltransferase
Reaction: a fatty acyl-[acyl-carrier protein] + an α-Kdo-(2→4)-α-Kdo-(2→6)-[lipid IVA] = an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)-[lipid IVA] + an [acyl-carrier protein]
For diagram of reaction, click here
Glossary: Kdo = 3-deoxy-D-manno-oct-2-ulopyranosylonic acid
a lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)-[lipid IVA] = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-(acyloxy)acyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phosphono-α-D-glucopyranose
Other name(s): LpxL; htrB (gene name); dodecanoyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-lipid IVA O-dodecanoyltransferase; lauroyl-[acyl-carrier protein]:Kdo2-lipid IVA O-lauroyltransferase; (Kdo)2-lipid IVA lauroyltransferase; α-Kdo-(2→4)-α-(2→6)-lipid IVA lauroyltransferase; dodecanoyl-[acyl-carrier protein]:Kdo2-lipid IVA O-dodecanoyltransferase; Kdo2-lipid IVA lauroyltransferase
Systematic name: fatty acyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-[lipid IVA] O-acyltransferase
Comments: The enzyme is involved in the biosynthesis of the phosphorylated outer membrane glycolipid lipid A. It transfers an acyl group to the 3-O position of the 3R-hydroxyacyl already attached to the nitrogen of the non-reducing glucosamine molecule. The enzyme from the bacterium Escherichia coli is specific for lauryl (C12) acyl groups, giving the enzyme its previous accepted name. However, enzymes from different species accept highly variable substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Clementz, T., Bednarski, J.J. and Raetz, C.R. Function of the htrB high temperature requirement gene of Escherichia coli in the acylation of lipid A: HtrB catalyzed incorporation of laurate. J. Biol. Chem. 271 (1996) 12095-12102. [PMID: 8662613]
2. van der Ley, P., Steeghs, L., Hamstra, H.J., ten Hove, J., Zomer, B. and van Alphen, L. Modification of lipid A biosynthesis in Neisseria meningitidis lpxL mutants: influence on lipopolysaccharide structure, toxicity, and adjuvant activity. Infect. Immun. 69 (2001) 5981-5990. [PMID: 11553534]
3. McLendon, M.K., Schilling, B., Hunt, J.R., Apicella, M.A. and Gibson, B.W. Identification of LpxL, a late acyltransferase of Francisella tularensis, Infect. Immun. 75 (2007) 5518-5531. [PMID: 17724076]
4. Six, D.A., Carty, S.M., Guan, Z. and Raetz, C.R. Purification and mutagenesis of LpxL, the lauroyltransferase of Escherichia coli lipid A biosynthesis. Biochemistry 47 (2008) 8623-8637. [PMID: 18656959]
5. Fathy Mohamed, Y., Hamad, M., Ortega, X.P. and Valvano, M.A. The LpxL acyltransferase is required for normal growth and penta-acylation of lipid A in Burkholderia cenocepacia, Mol. Microbiol. 104 (2017) 144-162. [PMID: 28085228]
Accepted name: acyl-Kdo2-lipid IVA acyltransferase
Reaction: a fatty acyl-[acyl-carrier protein] + an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)-[lipid IVA] = an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)2-[lipid IVA] + an [acyl-carrier protein]
For diagram of reaction click here
Glossary: Kdo = 3-deoxy-D-manno-oct-2-ulopyranosylonic acid
a lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)-[lipid IVA] = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-(acyloxy)acyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phosphono-α-D-glucopyranose
an α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)2-[lipid IVA] = 3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→4)-3-deoxy-α-D-manno-oct-2-ulopyranosyl-(2→6)-2-deoxy-2-{[(3R)-3-(acyloxy)acyl]amino}-3-O-[(3R)-3-(acyloxy)acyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
Other name(s): lpxM (gene name); MsbB acyltransferase; myristoyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-(dodecanoyl)-lipid IVA O-myristoyltransferase; tetradecanoyl-[acyl-carrier protein]:dodecanoyl-Kdo2-lipid IVA O-tetradecanoyltransferase; lauroyl-Kdo2-lipid IVA myristoyltransferase
Systematic name: fatty acyl-[acyl-carrier protein]:α-Kdo-(2→4)-α-Kdo-(2→6)-(acyl)-[lipid IVA] O-acyltransferase
Comments: The enzyme is involved in the biosynthesis of the phosphorylated outer membrane glycolipid lipid A. It transfers an acyl group to the 3-O position of the 3R-hydroxyacyl already attached at the 2-O position of the non-reducing glucosamine molecule. The enzyme from the bacterium Escherichia coli is specific for myristoyl (C14) acyl groups, giving the enzyme its previous accepted name. However, enzymes from different species accept highly variable substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Clementz, T., Zhou, Z. and Raetz, C.R. Function of the Escherichia coli msbB gene, a multicopy suppressor of htrB knockouts, in the acylation of lipid A. Acylation by MsbB follows laurate incorporation by HtrB. J. Biol. Chem. 272 (1997) 10353-10360. [PMID: 9099672]
2. Dovala, D., Rath, C.M., Hu, Q., Sawyer, W.S., Shia, S., Elling, R.A., Knapp, M.S. and Metzger, L.E., 4th. Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism. Proc. Natl. Acad. Sci. USA 113 (2016) E6064-E6071. [PMID: 27681620]
Accepted name: acyl-[acyl-carrier protein]—UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucopyranose N-acyltransferase
Reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] + UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucopyranose = an [acyl-carrier protein] + a UDP-2-acetamido-2,3-dideoxy-3-{[(3R)-3-hydroxyacyl]amino}-α-D-glucopyranose
Other name(s): lpxA (gene name) (ambiguous)
Systematic name: (3R)-3-hydroxyacyl-[acyl-carrier-protein]:UDP-2-acetamido-3-amino-2,3-dideoxy-α-D-glucopyranose 3-N-[(3R)-hydroxyacyl]transferase
Comments: The enzyme is found in bacterial species whose lipid A contains 2,3-diamino-2,3-dideoxy-D-glucopyranose. Some enzymes, such as that from Leptospira interrogans, are highly specific for 2,3-diamino-2,3-dideoxy-D-glucopyranose, while others, such as the enzyme from Acidithiobacillus ferrooxidans, are also able to accept UDP-N-acetyl-α-D-glucosamine (cf. EC 2.3.1.129, acyl-[acyl-carrier-protein]—UDP-N-acetylglucosamine O-acyltransferase). The enzymes from different organisms also differ in their specificity for the acyl donor. The enzyme from Leptospira interrogans is highly specific for (3R)-3-hydroxydodecanoyl-[acp], while that from Mesorhizobium loti functions almost equally well with 10-, 12-, and 14-carbon 3-hydroxyacyl-[acp]s.
References:
1. Sweet, C.R., Williams, A.H., Karbarz, M.J., Werts, C., Kalb, S.R., Cotter, R.J. and Raetz, C.R. Enzymatic synthesis of lipid A molecules with four amide-linked acyl chains. LpxA acyltransferases selective for an analog of UDP-N-acetylglucosamine in which an amine replaces the 3"-hydroxyl group. J. Biol. Chem. 279 (2004) 25411-25419. [PMID: 15044493]
2. Robins, L.I., Williams, A.H. and Raetz, C.R. Structural basis for the sugar nucleotide and acyl-chain selectivity of Leptospira interrogans LpxA. Biochemistry 48 (2009) 6191-6201. [PMID: 19456129]
Accepted name: acetyl-CoA:lysine N6-acetyltransferase
Reaction: acetyl-CoA + L-lysine = CoA + N6-acetyl-L-lysine
Other name(s): LYC1 (gene name); lysine N6-acetyltransferase (ambiguous)
Systematic name: acetyl-CoA:L-lysine N6-acetyltransferase
Comments: The enzyme catalyses the first step of an L-lysine degradation pathway found in many fungal species. The enzyme is specific for acetyl-CoA as the acetyl donor. cf. EC 2.3.1.32, lysine N-acetyltransferase.
References:
1. Schmidt, H., Bode, R., and Birnbaum , D. Lysine degradation in Candida maltosa: occurrence of a novel enzyme, acetyl-CoA: L-lysine N-acetyltransferase. Arch. Microbiol. 150 (1988) 215-218.
2. Large, P.J. and Robertson, A. The route of lysine breakdown in Candida tropicalis, FEMS Microbiol. Lett. 66 (1991) 209-213. [PMID: 1682209]
3. Bode, R., Thurau, A.M. and Schmidt, H. Characterization of acetyl-CoA: L-lysine N6-acetyltransferase, which catalyses the first step of carbon catabolism from lysine in Saccharomyces cerevisiae, Arch. Microbiol. 160 (1993) 397-400. [PMID: 8257283]
4. Beckerich, J.M., Lambert, M. and Gaillardin, C. LYC1 is the structural gene for lysine N-6-acetyl transferase in yeast. Curr. Genet. 25 (1994) 24-29. [PMID: 8082161]
Accepted name: 6-diazo-5-oxo-L-norleucine Nα-acetyltranferase
Reaction: acetyl-CoA + 6-diazo-5-oxo-L-norleucine = CoA + N-acetyl-6-diazo-5-oxo-L-norleucine
Other name(s): azpI (gene name)
Systematic name: acetyl-CoA:6-diazo-5-oxo-L-norleucine Nα-acetyltransferase
Comments: The enzyme, characterized from the bacterium Streptacidiphilus griseoplanus, participates in the biosynthesis of the tripeptide alazopeptin.
References:
1. Kawai, S., Sugaya, Y., Hagihara, R., Tomita, H., Katsuyama, Y. and Ohnishi, Y. Complete biosynthetic pathway of alazopeptin, a tripeptide consisting of two molecules of 6-diazo-5-oxo-L-norleucine and one molecule of alanine. Angew. Chem. Int. Ed. Engl. 60 (2021) 10319-10325. [PMID: 33624374]
Accepted name: (R)-citramalate synthase
Reaction: acetyl-CoA + pyruvate + H2O = CoA + (2R)-2-hydroxy-2-methylbutanedioate
Glossary: (2R)-2-hydroxy-2-methylbutanedioate = (2R)-2-methylmalate = (–)-citramalate
3-methyl-2-oxobutanoate =α-ketoisovalerate
2-oxobutanoate = α-ketobutyrate
4-methyl-2-oxopentanoate = α-ketoisocaproate
2-oxohexanoate = α-ketopimelate
2-oxoglutarate = α-ketoglutarate
Other name(s): CimA
Comments: One of the enzymes involved in a pyruvate-derived pathway for isoleucine biosynthesis that is found in some bacterial and archaeal species [1,2]. The enzyme can be inhibited by isoleucine, the end-product of the pathway, but not by leucine [2]. The enzyme is highly specific for pyruvate as substrate, as the 2-oxo acids 3-methyl-2-oxobutanoate, 2-oxobutanoate, 4-methyl-2-oxopentanoate, 2-oxohexanoate and 2-oxoglutarate cannot act as substrate [1,2].
References:
1. Howell, D.M., Xu, H. and White, R.H. (R)-citramalate synthase in methanogenic archaea. J. Bacteriol. 181 (1999) 331-333. [PMID: 9864346]
2. Xu, H., Zhang, Y., Guo, X., Ren, S., Staempfli, A.A., Chiao, J., Jiang, W. and Zhao, G. Isoleucine biosynthesis in Leptospira interrogans serotype 1ai strain 56601 proceeds via a threonine-independent pathway. J. Bacteriol. 186 (2004) 5400-5409. [PMID: 15292141]
Accepted name: sterol 27-β-glucosyltransferase
Reaction: UDP-α-D-glucose + a 27-hydroxysteroid = UDP + a sterol 27-β-D-glucoside
For diagram of reaction, click here
Systematic name: UDP-α-D-glucose:sterol 27-O-β-D-glucosyltransferase
Comments: The enzyme, isolated from the plant Withania somnifera (ashwagandha), transfers D-glucose to a β-hydroxyl group present at the C-27 position in sterols/withanolides, provided the substrate possesses a 17α-OH group. Natural substrates are 17α-hydroxywithaferin A, 27β-hydroxywithanone, and 5α,6β,17α,27β-tetrahydroxywithanolide. The enzyme's activity with withanolide A and withanolide U, which lack a 17α-hydroxyl group, suggests it may also be able to glucosylate the C-20 β-OH position, although this has not been verified yet. The enzyme does not glucosylate sterols at the C-3 position.
References:
1. Madina, B.R., Sharma, L.K., Chaturvedi, P., Sangwan, R.S. and Tuli, R. Purification and characterization of a novel glucosyltransferase specific to 27β-hydroxy steroidal lactones from Withania somnifera and its role in stress responses. Biochim. Biophys. Acta 1774 (2007) 1199-1207. [PMID: 17704015]
Accepted name: GlcNAc-β-1,3-Gal β-1,6-N-acetylglucosaminyltransferase (distally acting)
Reaction: UDP-N-acetyl-α-D-glucosamine + β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-GlcNAc-R = UDP + β-D-GlcNAc-(1→3)-[β-D-GlcNAc-(1→6)]-β-D-Gal-(1→4)-β-D-GlcNAc-R
Other name(s): UDP-GlcNAc:GlcNAcβ1-3Gal(-R) β1-6(GlcNAc to Gal) N-acetylglucosaminyltransferase; dIGnT; C2GnT2 (misleading)
Systematic name: UDP-N-acetyl-α-D-glucosamine:N-acetyl-β-D-glucosaminyl-(1→3)-β-D-galactosyl-(1→4)-N-acetyl-β-D-glucosaminide 6-β-N-acetylglucosaminyltransferase (configuration-inverting)
Comments: Involved in the production of milk oligosaccharides in the lacto-N-triose (LNT) series. Cf. EC 2.4.1.150 (N-acetyllactosaminide β-1,6-N-acetylglucosaminyltransferase; cIGnT) and EC 2.4.1.148 (acetylgalactosaminyl-O-glycosyl-glycoprotein β-1,6-N-acetylglucosaminyltransferase).
References:
1. Piller, F., Cartron, J.P., Maranduba, A., Veyrieres, A., Leroy, Y. and Fournet, B. Biosynthesis of blood group I antigens. Identification of a UDP-GlcNAc:GlcNAc β 1-3Gal(-R) β 1-6(GlcNAc to Gal) N-acetylglucosaminyltransferase in hog gastric mucosa. J. Biol. Chem. 259 (1984) 13385-13390. [PMID: 6490658]
2. Yeh, J.C., Ong, E. and Fukuda, M. Molecular cloning and expression of a novel β-1,6-N-acetylglucosaminyltransferase that forms core 2, core 4, and I branches. J. Biol. Chem. 274 (1999) 3215-3221. [PMID: 9915862]
Accepted name: (Kdo)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase
Reaction: CMP-β-Kdo + an α-Kdo-(2→6)-[lipid IVA] = CMP + an α-Kdo-(2→4)-α-Kdo-(2→6)-[lipid IVA]
For diagram of reaction click here
Glossary: CMP-β-Kdo = CMP-3-deoxy-β-D-manno-oct-2-ulopyranosylonate
a lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
Other name(s): waaA (gene name); kdtA (gene name); 3-deoxy-D-manno-oct-2-ulosonic acid transferase; 3-deoxy-manno-octulosonic acid transferase; (KDO)-lipid IVA 3-deoxy-D-manno-octulosonic acid transferase; CMP-3-deoxy-D-manno-oct-2-ulosonate:(Kdo)-lipid IVA 3-deoxy-D-manno-oct-2-ulosonate transferase; Kdo transferase (ambiguous)
Systematic name: CMP-3-deoxy-β-D-manno-oct-2-ulosonate:α-Kdo-(2→6)-[lipid IVA] 3-deoxy-D-manno-oct-2-ulosonate transferase (configuration-inverting)
Comments: The enzyme from Escherichia coli is bifunctional and transfers two 3-deoxy-D-manno-oct-2-ulosonate residues to lipid IVA (cf. EC 2.4.99.12 [lipid IVA 3-deoxy-D-manno-octulosonic acid transferase]) [1]. The enzymes from Chlamydia transfer three or more 3-deoxy-D-manno-oct-2-ulosonate residues and generate genus-specific epitopes [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Belunis, C.J. and Raetz, C.R. Biosynthesis of endotoxins. Purification and catalytic properties of 3-deoxy-D-manno-octulosonic acid transferase from Escherichia coli, J. Biol. Chem. 267 (1992) 9988-9997. [PMID: 1577828]
2. Lobau, S., Mamat, U., Brabetz, W. and Brade, H. Molecular cloning, sequence analysis, and functional characterization of the lipopolysaccharide biosynthetic gene kdtA encoding 3-deoxy-α-D-manno-octulosonic acid transferase of Chlamydia pneumoniae strain TW-183. Mol. Microbiol. 18 (1995) 391-399. [PMID: 8748024]
3. Schmidt, H., Hansen, G., Singh, S., Hanuszkiewicz, A., Lindner, B., Fukase, K., Woodard, R.W., Holst, O., Hilgenfeld, R., Mamat, U. and Mesters, J.R. Structural and mechanistic analysis of the membrane-embedded glycosyltransferase WaaA required for lipopolysaccharide synthesis. Proc. Natl. Acad. Sci. USA 109 (2012) 6253-6258. [PMID: 22474366]
Accepted name: alkylcobalamin dealkylase
Reaction: (1) methylcob(III)alamin + [alkylcobalamin dealkylase] + glutathione = cob(I)alamin-[alkylcobalamin dealkylase] + an S-methyl glutathione
(2) adenosylcob(III)alamin + [alkylcobalamin dealkylase] + glutathione = cob(I)alamin-[alkylcobalamin dealkylase] + S-adenosyl glutathione
Other name(s): MMACHC (gene name); alkylcobalamin:glutathione S-alkyltransferase; alkylcobalamin reductase
Systematic name: methylcobalamin:glutathione S-methyltransferase
Comments: This mammalian enzyme, which is cytosolic, can bind internalized methylcob(III)alamin and adenosylcob(III)alamin and process them to cob(I)alamin using the thiolate of glutathione for nucleophilic displacement. The product remains bound to the protein, and, following its oxidation to cob(II)alamin, is transferred by the enzyme, together with its interacting partner MMADHC, directly to downstream enzymes involved in adenosylcob(III)alamin and methylcob(III)alamin biosynthesis. In addition to its dealkylase function, the enzyme also catalyse an entirely different decyanase reaction with cyanocob(III)alamin (cf. EC 1.16.1.6, cyanocobalamin reductase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Hannibal, L., Kim, J., Brasch, N.E., Wang, S., Rosenblatt, D.S., Banerjee, R. and Jacobsen, D.W. Processing of alkylcobalamins in mammalian cells: A role for the MMACHC (cblC) gene product. Mol. Genet. Metab. 97 (2009) 260-266. [PMID: 19447654]
2. Kim, J., Hannibal, L., Gherasim, C., Jacobsen, D.W. and Banerjee, R. A human vitamin B12 trafficking protein uses glutathione transferase activity for processing alkylcobalamins. J. Biol. Chem. 284 (2009) 33418-33424. [PMID: 19801555]
3. Koutmos, M., Gherasim, C., Smith, J.L. and Banerjee, R. Structural basis of multifunctionality in a vitamin B12-processing enzyme. J. Biol. Chem. 286 (2011) 29780-29787. [PMID: 21697092]
Accepted name: corrinoid adenosyltransferase EutT
Reaction: 2 ATP + 2 cob(II)alamin + a reduced flavoprotein = 2 diphosphate + 2 phosphate + 2 adenosylcob(III)alamin + an oxidized flavoprotein (overall reaction)
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
(1b) a reduced flavoprotein + 2 [corrinoid adenosyltransferase]-cob(II)alamin = an oxidized flavoprotein + 2 [corrinoid adenosyltransferase]-cob(I)alamin (spontaneous)
(1c) 2 ATP + 2 [corrinoid adenosyltransferase]-cob(I)alamin = 2 diphosphate + 2 phosphate + 2 adenosylcob(III)alamin + 2 [corrinoid adenosyltransferase]
Other name(s): eutT (gene name)
Systematic name: ATP:cob(II)alamin Coβ-adenosyltransferase (diphosphate-forming)
Comments: The corrinoid adenosylation pathway comprises three steps: (i) reduction of Co(III) within the corrinoid to Co(II) by a one-electron transfer. This can occur non-enzymically in the presence of dihydroflavin nucleotides or reduced flavoproteins [1]. (ii) Co(II) is bound by corrinoid adenosyltransferase, resulting in displacement of the lower axial ligand by an aromatic residue. The reduction potential of the 4-coordinate Co(II) intermediate is raised by ~250 mV compared with the free compound, bringing it to within physiological range. This is followed by a second single-electron transfer from either free dihydroflavins or the reduced flavin cofactor of flavoproteins, resulting in reduction to Co(I) [4]. (iii) the Co(I) conducts a nucleophilic attack on the adenosyl moiety of ATP, resulting in transfer of the deoxyadenosyl group and oxidation of the cobalt atom to Co(III) state. Three types of corrinoid adenosyltransferases, not related by sequence, have been described. In the anaerobic bacterium Salmonella enterica they are encoded by the cobA gene (a housekeeping enzyme involved in both the de novo biosynthesis and the salvage of adenosylcobalamin), the pduO gene (involved in (S)-propane-1,2-diol utilization), and the eutT gene (involved in ethanolamine utilization). The first two types, which produce triphosphate, are classified as EC 2.5.1.17, corrinoid adenosyltransferase, while the EutT type hydrolyses triphosphate to diphosphate and phosphate during catalysis and is thus classified separately.
References:
1. Fonseca, M.V. and Escalante-Semerena, J.C. Reduction of cob(III)alamin to cob(II)alamin in Salmonella enterica serovar typhimurium LT2. J. Bacteriol. 182 (2000) 4304-4309. [PMID: 10894741]
2. Sheppard, D.E., Penrod, J.T., Bobik, T., Kofoid, E. and Roth, J.R. Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica, J. Bacteriol. 186 (2004) 7635-7644. [PMID: 15516577]
3. Buan, N.R. and Escalante-Semerena, J.C. Purification and initial biochemical characterization of ATP:cob(I)alamin adenosyltransferase (EutT) enzyme of Salmonella enterica, J. Biol. Chem. 281 (2006) 16971-16977. [PMID: 16636051]
4. Mera, P.E. and Escalante-Semerena, J.C. Dihydroflavin-driven adenosylation of 4-coordinate Co(II) corrinoids: are cobalamin reductases enzymes or electron transfer proteins. J. Biol. Chem. 285 (2010) 2911-2917. [PMID: 19933577]
5. Moore, T.C., Mera, P.E. and Escalante-Semerena, J.C. the Eutt enzyme of Salmonella enterica is a unique ATP:cob(I)alamin adenosyltransferase metalloprotein that requires ferrous ions for maximal activity. J. Bacteriol. 196 (2014) 903-910. [PMID: 24336938]
Accepted name: 4-aminobutyrate—2-oxoglutarate transaminase
Reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
For diagram of reaction click here
Glossary: 4-aminobutanoate = γ-aminobutyrate = GABA
Other name(s): β-alanine-oxoglutarate transaminase; aminobutyrate aminotransferase (ambiguous); β-alanine aminotransferase; β-alanine-oxoglutarate aminotransferase; γ-aminobutyrate aminotransaminase (ambiguous); γ-aminobutyrate transaminase (ambiguous); γ-aminobutyrate-α-ketoglutarate aminotransferase; γ-aminobutyrate-α-ketoglutarate transaminase; γ-aminobutyrate:α-oxoglutarate aminotransferase; γ-aminobutyric acid aminotransferase (ambiguous); γ-aminobutyric acid transaminase (ambiguous); γ-aminobutyric acid-α-ketoglutarate transaminase; γ-aminobutyric acid-α-ketoglutaric acid aminotransferase; γ-aminobutyric acid-2-oxoglutarate transaminase; γ-aminobutyric transaminase (ambiguous); 4-aminobutyrate aminotransferase (ambiguous); 4-aminobutyrate-2-ketoglutarate aminotransferase; 4-aminobutyrate-2-oxoglutarate aminotransferase; 4-aminobutyrate-2-oxoglutarate transaminase; 4-aminobutyric acid 2-ketoglutaric acid aminotransferase; 4-aminobutyric acid aminotransferase (ambiguous); aminobutyrate transaminase (ambiguous); GABA aminotransferase (ambiguous); GABA transaminase (ambiguous); GABA transferase (ambiguous); GABA-α-ketoglutarate aminotransferase; GABA-α-ketoglutarate transaminase; GABA-α-ketoglutaric acid transaminase; GABA-α-oxoglutarate aminotransferase; GABA-2-oxoglutarate aminotransferase; GABA-2-oxoglutarate transaminase; GABA-oxoglutarate aminotransferase; GABA-oxoglutarate transaminase; glutamate-succinic semialdehyde transaminase; GabT
Systematic name: 4-aminobutanoate:2-oxoglutarate aminotransferase
Comments: Requires pyridoxal phosphate. Some preparations also act on β-alanine, 5-aminopentanoate and (R,S)-3-amino-2-methylpropanoate. cf. EC 2.6.1.120, β-alanine—2-oxoglutarate transaminase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9037-67-6
References:
1. Scott, E.M. and Jakoby, W.B. Soluble γ-aminobutyric-glutamic transaminase from Pseudomonas fluorescens, J. Biol. Chem. 234 (1959) 932-936. [PMID: 13654294]
2. Aurich, H. Über die β-Alanin-α-Ketoglutarat-Transaminase aus Neurospora crassa, Hoppe-Seyler's Z. Physiol. Chem. 326 (1961) 25-33. [PMID: 13863304]
3. Schausboe, A., Wu, J.-Y. and Roberts, E. Purification and characterization of the 4-aminobutyrate-2-ketoglutarate transaminase from mouse brain. Biochemistry 12 (1973) 2868-2873. [PMID: 4719123]
4. Bartsch, K., von Johnn-Marteville, A. and Schulz, A. Molecular analysis of two genes of the Escherichia coli gab cluster: nucleotide sequence of the glutamate:succinic semialdehyde transaminase gene (gabT) and characterization of the succinic semialdehyde dehydrogenase gene (gabD). J. Bacteriol. 172 (1990) 7035-7042. [PMID: 2254272]
Accepted name: β-alanine—2-oxoglutarate transaminase
Reaction: β-alanine + 2-oxoglutarate = 3-oxopropanoate + L-glutamate
For diagram of reaction, click here
Other name(s): pydD (gene name); β-alanine aminotransferase
Systematic name: β-alanine:2-oxoglutarate aminotransferase
Comments: The enzyme, found in many Gram-positive bacteria, participates in the reductive degradation of pyrimidines. In eukaryotes this activity is catalysed by EC 2.6.1.19, 4-aminobutyrate—2-oxoglutarate transaminase.
References:
1. Fujimoto, S., Mizutani, N., Mizota, C. and Tamaki, N. The level of β-alanine aminotransferase activity in regenerating and differentiating rat liver. Biochim. Biophys. Acta 882 (1986) 106-112. [PMID: 3085724]
2. Yin, J., Wei, Y., Liu, D., Hu, Y., Lu, Q., Ang, E.L., Zhao, H. and Zhang, Y. An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. J. Biol. Chem. 294 (2019) 15662-15671. [PMID: 31455636]
Accepted name: 8-amino-7-oxononanoate carboxylating dehydrogenase
Reaction: (8S)-8-amino-7-oxononanoate + [protein]-L-lysine + CO2 = (7R,8S)-8-amino-7-(carboxyamino)nonanoate + [protein]-(S)-2-amino-6-oxohexanoate (overall reaction)
(1a) (8S)-8-amino-7-oxononanoate + [protein]-L-lysine + NAD(P)H = [protein]-N6-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-lysine + H2O + NAD(P)+
(1b) [protein]-N6-[(2S,3R)-2-amino-8-carboxyoctan-3-yl]-L-lysine + CO2 + H2O + NAD(P)+ + H+ = (7R,8S)-8-amino-7-(carboxyamino)nonanoate + [protein]-(S)-2-amino-6-oxohexanoate + NAD(P)H + H+
Other name(s): bioU (gene name)
Systematic name: (8S)-8-amino-7-oxononanoate:[protein]-L-lysine aminotransferase (N-carboxylating)
Comments: The enzyme, which participates in biotin biosynthesis, is found in haloarchaea and some cyanobacteria. It forms a conjugant between (7R,8S)-8-amino-7-oxononanoate and an internal lysine residue and catalyses multiple reactions, including a reduction, a carboxylation of the ε-amino group of the lysine residue, and an oxidative cleavage of the conjugate to release (7R,8S)-8-amino-7-(carboxyamino)nonanoate. During this process the lysine residue serves as an amino donor and is converted to (S)-2-amino-6-oxohexanoate, resulting in inactivation of the enzyme following a single turnover. cf. EC 2.6.1.105, lysine—8-amino-7-oxononanoate transaminase.
References:
1. Sakaki, K., Ohishi, K., Shimizu, T., Kobayashi, I., Mori, N., Matsuda, K., Tomita, T., Watanabe, H., Tanaka, K., Kuzuyama, T. and Nishiyama, M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat. Chem. Biol. 16 (2020) 415-422. [PMID: 32042199]
Accepted name: UDP-N-acetyl-3-dehydro-α-D-glucosamine 3-aminotranferase
Reaction: UDP-3-acetamido-2-amino-2,3-dideoxy-α-D-glucopyranose + 2-oxoglutarate = UDP-N-acetyl-3-dehydro-α-D-glucosamine + L-glutamate
Other name(s): gnnB (gene name)
Systematic name: UDP-3-acetamido-2-amino-2,3-dideoxy-α-D-glucopyranose:2-oxoglutarate aminotransferase
Comments: This bacterial enzyme participates, together with EC 1.1.1.374, UDP-N-acetylglucosamine 3-dehydrogenase, in the synthesis of 2,3-diamino-2,3-dideoxy-D-glucopyranose, a component of lipid A in some species.
References:
1. Sweet, C.R., Ribeiro, A.A. and Raetz, C.R. Oxidation and transamination of the 3"-position of UDP-N-acetylglucosamine by enzymes from Acidithiobacillus ferrooxidans. Role in the formation of lipid a molecules with four amide-linked acyl chains. J. Biol. Chem. 279 (2004) 25400-25410. [PMID: 15044494]
Accepted name: 4-amino-4-deoxychorismate synthase (2-amino-4-deoxychorismate-forming)
Reaction: chorismate + 2 L-glutamine + H2O = 4-amino-4-deoxychorismate + 2 L-glutamate + ammonia (overall reaction)
(1a) chorismate + L-glutamine = (2S)-2-amino-4-deoxychorismate + L-glutamate
(1b) (2S)-2-amino-4-deoxychorismate + L-glutamine + H2O = 4-amino-4-deoxychorismate + L-glutamate + ammonia
Other name(s): ADCS (ambiguous); ADC synthase (ambiguous)
Systematic name: chorismate:L-glutamine aminotransferase (2-amino-4-deoxychorismate-forming)
Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is a heterodimer. The PabA component is a glutamine amidotransferase that hydrolyses glutamine to glutamate, forming ammonia, which is channeled to the PabB active site. PabB catalyses the formation of 4-amino-4-deoxychorismate from chorismate in two steps, via the intermediate 2-amino-4-deoxychorismate. cf. EC 2.6.1.85, aminodeoxychorismate synthase.
References:
1. Schadt, H.S., Schadt, S., Oldach, F. and Sussmuth, R.D. 2-Amino-2-deoxyisochorismate is a key intermediate in Bacillus subtilis p-aminobenzoic acid biosynthesis. J. Am. Chem. Soc. 131 (2009) 3481-3483. [PMID: 19275258]
2. Bera, A.K., Atanasova, V., Dhanda, A., Ladner, J.E. and Parsons, J.F. Structure of aminodeoxychorismate synthase from Stenotrophomonas maltophilia, Biochemistry 51 (2012) 10208-10217. [PMID: 23230967]
Accepted name: tetraacyldisaccharide 4'-kinase
Reaction: ATP + a lipid A disaccharide = ADP + a lipid IVA
For diagram of reaction click here
Glossary: a lipid A disaccharide = a dephospho-lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
a lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose
Other name(s): lpxK (gene name); lipid-A 4'-kinase; ATP:2,2',3,3'-tetrakis[(3R)-3-hydroxytetradecanoyl]-β-D-glucosaminyl-(1→6)-α-D-glucosaminyl-phosphate 4'-O-phosphotransferase
Systematic name: ATP:2-deoxy-2-{[(3R)-3-hydroxyacyl]amino}-3-O-[(3R)-3-hydroxyacyl]-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyacyl]-2-{[(3R)-3-hydroxyacyl]amino}-1-O-phospho-α-D-glucopyranose 4'-O-phosphotransferase
Comments: Involved with EC 2.3.1.129 (acyl-[acyl-carrier-protein]—UDP-N-acetylglucosamine O-acyltransferase) and EC 2.4.1.182 (lipid-A-disaccharide synthase) in the biosynthesis of the phosphorylated glycolipid, lipid A, in the outer membrane of Gram-negative bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 107309-06-8
References:
1. Ray, B.L. and Raetz, C.R.H. The biosynthesis of gram-negative endotoxin. A novel kinase in Escherichia coli membranes that incorporates the 4'-phosphate of lipid A. J. Biol. Chem. 262 (1987) 1122-1128. [PMID: 3027079]
2. Emptage, R.P., Daughtry, K.D., Pemble, C.W., 4th and Raetz, C.R. Crystal structure of LpxK, the 4'-kinase of lipid A biosynthesis and atypical P-loop kinase functioning at the membrane interface. Proc. Natl. Acad. Sci. USA 109 (2012) 12956-12961. [PMID: 22826246]
3. Emptage, R.P., Pemble, C.W., 4th, York, J.D., Raetz, C.R. and Zhou, P. Mechanistic characterization of the tetraacyldisaccharide-1-phosphate 4'-kinase LpxK involved in lipid A biosynthesis. Biochemistry 52 (2013) 2280-2290. [PMID: 23464738]
4. Emptage, R.P., Tonthat, N.K., York, J.D., Schumacher, M.A. and Zhou, P. Structural basis of lipid binding for the membrane-embedded tetraacyldisaccharide-1-phosphate 4'-kinase LpxK. J. Biol. Chem. 289 (2014) 24059-24068. [PMID: 25023290]
Accepted name: D-tagatose-1-phosphate kinase
Reaction: ATP + D-tagatose 1-phosphate = ADP + D-tagatose 1,6-bisphosphate
Other name(s): TagK
Systematic name: ATP:D-tagatose-1-phosphate 6-phosphotransferase
Comments: The enzyme has been pruified from the bacterium Bacillus licheniformis and is part of a D-tagatose catabolic pathway.
References:
1. Van der Heiden, E., Delmarcelle, M., Simon, P., Counson, M., Galleni, M., Freedberg, D.I., Thompson, J., Joris, B. and Battistel, M.D. Synthesis and physicochemical characterization of D-tagatose-1-phosphate: the substrate of the tagatose-1-phosphate kinase in the phosphotransferase system-mediated D-tagatose catabolic pathway of Bacillus licheniformis, J. Mol. Microbiol. Biotechnol. 25 (2015) 106-119. [PMID: 26159072]
Accepted name: lipopolysaccharide core heptose(I) kinase
Reaction: ATP + an α-Hep-(1→3)-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A] = ADP + an α-Hep-(1→3)-4-O-phospho-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A]
Glossary: Lipid A is a lipid component of the lipopolysaccharides (LPS) of Gram-negative bacteria. It usually consists of two glucosamine units connected by a β(1→6) bond and decorated with four to seven acyl chains and up to two phosphate groups.
Hep = L-glycero-β-D-manno-heptose.
Other name(s): WaaP; RfaP
Systematic name: ATP:an α-Hep-(1→3)-α-Hep-(1→5)-[α-Kdo-(2→4)]-α-Kdo-(2→6)-[lipid A] heptoseI 4-O-phosphotransferase
Comments: The enzyme catalyses the phosphorylation of L-glycero-D-manno-heptose I (the first heptose added to the lipid, Hep I) in the biosynthesis of the inner core oligosaccharide of the lipopolysaccharide (endotoxin) of some Gram-negative bacteria.
References:
1. Yethon, J.A. and Whitfield, C. Purification and characterization of WaaP from Escherichia coli, a lipopolysaccharide kinase essential for outer membrane stability. J. Biol. Chem. 276 (2001) 5498-5504. [PMID: 11069912]
2. Zhao, X. and Lam, J.S. WaaP of Pseudomonas aeruginosa is a novel eukaryotic type protein-tyrosine kinase as well as a sugar kinase essential for the biosynthesis of core lipopolysaccharide. J. Biol. Chem. 277 (2002) 4722-4730. [PMID: 11741974]
3. Kreamer, N.NK., Chopra, R., Caughlan, R.E., Fabbro, D., Fang, E., Gee, P., Hunt, I., Li, M., Leon, B.C., Muller, L., Vash, B., Woods, A.L., Stams, T., Dean, C.R. and Uehara, T. Acylated-acyl carrier protein stabilizes the Pseudomonas aeruginosa WaaP lipopolysaccharide heptose kinase. Sci. Rep. 8 (2018) 14124. [PMID: 30237436]
Accepted name: (2-aminoethyl)phosphonate cytidylyltransferase
Reaction: CTP + (2-aminoethyl)phosphonate = diphosphate + CMP-(2-aminoethyl)phosphonate
Other name(s): pntC (gene name)
Systematic name: CTP:(2-aminoethyl)phosphonate cytidylyltransferase
Comments: This bacterial enzyme activates (2-aminoethyl)phosphonate for incorporation into cell wall phosphonoglycans and phosphonolipids, much like EC 2.7.7.15, choline-phosphate cytidylyltransferase, activates phosphocholine for the same purpose.
References:
1. Rice, K., Batul, K., Whiteside, J., Kelso, J., Papinski, M., Schmidt, E., Pratasouskaya, A., Wang, D., Sullivan, R., Bartlett, C., Weadge, J.T., Van der Kamp, M.W., Moreno-Hagelsieb, G., Suits, M.D. and Horsman, G.P. The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Nat. Commun. 10 (2019) 3698. [PMID: 31420548]
Accepted name: bacterial tyrosine kinase
Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Other name(s): BY-kinase; bacterial protein tyrosine kinase
Systematic name: ATP:[protein]-L-tyrosine O-phosphotransferase (bacterial-type)
Comments: This family of enzymes includes most of the bacterial tyrosine kinases. These enzymes do not share sequence or structural homology with eukaryotic tyrosine kinases, and exploit ATP/GTP-binding Walker motifs to catalyse autophosphorylation and substrate phosphorylation on tyrosine. Two subfamilies have been defined: P-type enzymes contain an N-terminal transmembrane portion and an extracellular hairpin loop domain. The intracellular portion comprises the catalytic domain and a tyrosine-rich C-terminal domain that contains the site for autophosphorylation. In F-type enzymes the extracellular transmembrane domain and the intracellular catalytic domain are two independent proteins encoded by two separate genes. The majority of characterized bacterial tyrosine kinases regulate the production and export of capsular and extracellular polysaccharides, but other members are involved in many other functions.
References:
1. Grangeasse, C., Doublet, P., Vaganay, E., Vincent, C., Deleage, G., Duclos, B. and Cozzone, A.J. Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase. Gene 204 (1997) 259-265. [PMID: 9434192]
2. Wugeditsch, T., Paiment, A., Hocking, J., Drummelsmith, J., Forrester, C. and Whitfield, C. Phosphorylation of Wzc, a tyrosine autokinase, is essential for assembly of group 1 capsular polysaccharides in Escherichia coli, J. Biol. Chem. 276 (2001) 2361-2371. [PMID: 11053445]
3. Soulat, D., Jault, J.M., Duclos, B., Geourjon, C., Cozzone, A.J. and Grangeasse, C. Staphylococcus aureus operates protein-tyrosine phosphorylation through a specific mechanism. J. Biol. Chem. 281 (2006) 14048-14056. [PMID: 16565080]
4. Lee, D.C., Zheng, J., She, Y.M. and Jia, Z. Structure of Escherichia coli tyrosine kinase Etk reveals a novel activation mechanism. EMBO J. 27 (2008) 1758-1766. [PMID: 18497741]
5. Chao, J.D., Wong, D. and Av-Gay, Y. Microbial protein-tyrosine kinases. J. Biol. Chem. 289 (2014) 9463-9472. [PMID: 24554699]
Accepted name: S-methyl-1-thioxylulose 5-phosphate methylthiotransferase
Reaction: S-methyl-1-thio-D-xylulose 5-phosphate + glutathione = 1-deoxy-D-xylulose 5-phosphate + S-(methylsulfanyl)glutathione
Other name(s): 1-methylthioxylulose 5-phosphate sulfurylase (incorrect)
Systematic name: S-methyl-1-thio-D-xylulose 5-phosphate:glutathione methylthiotransferase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, belongs to the cupin superfamily and contains a manganese ion. It participates in an anaerobic salvage pathway that restores methionine from S-methyl-5'-thioadenosine. The enzyme was assayed in vitro using L-dithiothreitol instead of glutathione.
References:
1. 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]
2. Warlick, B.P., Evans, B.S., Erb, T.J., Ramagopal, U.A., Sriram, J., Imker, H.J., Sauder, J.M., Bonanno, J.B., Burley, S.K., Tabita, F.R., Almo, S.C., Sweedler, J.S. and Gerlt, J.A. 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum, Biochemistry 51 (2012) 8324-8326. [PMID: 23035785]
3. Cho, K., Evans, B.S., Wood, B.M., Kumar, R., Erb, T.J., Warlick, B.P., Gerlt, J.A. and Sweedler, J.V. Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. Metabolomics 2014 (2014) . [PMID: 25705145]
Accepted name: neryl diphosphate diphosphatase
Reaction: neryl diphosphate + H2O = nerol + diphosphate
For diagram of reaction, click here
Glossary: nerol = (2Z)-3,7-dimethylocta-2,6-dien-1-ol
Other name(s): NES (gene name); nerol synthase
Systematic name: neryl-diphosphate diphosphohydrolase
Comments: The enzyme, characterized from Glycine max (soybeans), is specific for neryl diphosphate.
References:
1. Zhang, M., Liu, J., Li, K. and Yu, D. Identification and characterization of a novel monoterpene synthase from soybean restricted to neryl diphosphate precursor. PLoS One 8 (2013) e75972. [PMID: 24124526]
[EC 3.2.1.66 Deleted entry: The activity is covered by EC 3.2.1.40, α-L-rhamnosidase (EC 3.2.1.66 created 1972, deleted 2021)]
[EC 3.2.1.134 Transferred entry: difructose-dianhydride-I hydrolase. Now EC 4.2.1.179, difructose-dianhydride-I hydro-lyase (EC 3.2.1.134 created 1992, deleted 2021)]
Accepted name: arabinogalactan exo α-(1,3)-α-D-galactosyl-(1→3)-L-arabinofuranosidase (non-reducing end)
Reaction: Hydrolysis of α-D-Galp-(1→3)-L-Araf disaccharides from non-reducing terminals in branches of type II arabinogalactan attached to proteins.
Glossary: Araf = arabinofuranose
Arap = arabinopyranose
Galp = galactopyranose
Other name(s): 3-O-α-D-galactosyl-α-L-arabinofuranosidase
Systematic name: type II arabinogalactan exo α-(1,3)-[α-D-galactosyl-(1→3)-L-arabinofuranose] hydrolase (non-reducing end)
Comments: The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses α-D-Galp-(1→3)-L-Araf disaccharides from the non-reducing terminal of arabinogalactan using an exo mode of action. It is particularly active with gum arabic arabinogalactan, a type II arabinogalactan produced by acacia trees. The enzyme can also hydrolyse β-L-Arap-(1→3)-L-Araf disaccharides, but this activity is significantly lower.
References:
1. Sasaki, Y., Horigome, A., Odamaki, T., Xiao, J.Z., Ishiwata, A., Ito, Y., Kitahara, K. and Fujita, K. Characterization of a novel 3-O-α-D-galactosyl-α-L-arabinofuranosidase for the assimilation of gum arabic AGP in Bifidobacterium longum subsp. longum, Appl. Environ. Microbiol. (2021) . [PMID: 33674431]
Accepted name: glutathione-S-conjugate glycine hydrolase
Reaction: a glutathione-S-conjugate + H2O = a [γ-glutamyl-L-cysteine]-S-conjugate + glycine
Other name(s): PCS1 (gene name); PRC1 (gene name); CPC (gene name); ATG42 (gene name); alr0975 (locus name)
Systematic name: glutathione-S-conjugate glycine hydrolase
Comments: The enzyme participates in a glutathione-mediated detoxification pathway found in plants, algae, fungi, and some bacteria. The enzymes from the plant Arabidopsis thaliana and the yeast Saccharomyces cerevisiae also catalyse the activity of EC 2.3.2.15, glutathione γ-glutamylcysteinyltransferase (phytochelatin synthase).
References:
1. Beck, A., Lendzian, K., Oven, M., Christmann, A. and Grill, E. Phytochelatin synthase catalyzes key step in turnover of glutathione conjugates. Phytochemistry 62 (2003) 423-431. [PMID: 12620355]
2. Grzam, A., Tennstedt, P., Clemens, S., Hell, R. and Meyer, A.J. Vacuolar sequestration of glutathione S-conjugates outcompetes a possible degradation of the glutathione moiety by phytochelatin synthase. FEBS Lett. 580 (2006) 6384-6390. [PMID: 17097087]
3. Harada, E., von Roepenack-Lahaye, E. and Clemens, S. A cyanobacterial protein with similarity to phytochelatin synthases catalyzes the conversion of glutathione to γ-glutamylcysteine and lacks phytochelatin synthase activity. Phytochemistry 65 (2004) 3179-3185. [PMID: 15561184]
4. Tsuji, N., Nishikori, S., Iwabe, O., Shiraki, K., Miyasaka, H., Takagi, M., Hirata, K. and Miyamoto, K. Characterization of phytochelatin synthase-like protein encoded by alr0975 from a prokaryote, Nostoc sp. PCC 7120. Biochem. Biophys. Res. Commun. 315 (2004) 751-755. [PMID: 14975765]
5. Vivares, D., Arnoux, P. and Pignol, D. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc. Natl. Acad. Sci. USA 102 (2005) 18848-18853. [PMID: 16339904]
6. Wunschmann, J., Krajewski, M., Letzel, T., Huber, E.M., Ehrmann, A., Grill, E. and Lendzian, K.J. Dissection of glutathione conjugate turnover in yeast. Phytochemistry 71 (2010) 54-61. [PMID: 19897216]
Accepted name: UDP-3-O-acyl-N-acetylglucosamine deacetylase
Reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-α-D-glucosamine + H2O = a UDP-3-O-[(3R)-3-hydroxyacyl]-α-D-glucosamine + acetate
For diagram of reaction click here
Other name(s): LpxC protein; LpxC enzyme; LpxC deacetylase; deacetylase LpxC; UDP-3-O-acyl-GlcNAc deacetylase; UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; UDP-(3-O-acyl)-N-acetylglucosamine deacetylase; UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase; UDP-(3-O-(R-3-hydroxymyristoyl))-N-acetylglucosamine deacetylase; UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetylglucosamine amidohydrolase
Systematic name: UDP-3-O-[(3R)-3-hydroxyacyl]-N-acetyl-α-D-glucosamine amidohydrolase
Comments: A zinc protein. The enzyme catalyses a committed step in the biosynthesis of lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Hernick, M., Gennadios, H.A., Whittington, D.A., Rusche, K.M., Christianson, D.W. and Fierke, C.A. UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism. J. Biol. Chem. 280 (2005) 16969-16978. [PMID: 15705580]
2. Jackman, J.E., Raetz, C.R. and Fierke, C.A. UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase of Escherichia coli is a zinc metalloenzyme. Biochemistry 38 (1999) 1902-1911. [PMID: 10026271]
3. Hyland, S.A., Eveland, S.S. and Anderson, M.S. Cloning, expression, and purification of UDP-3-O-acyl-GlcNAc deacetylase from Pseudomonas aeruginosa: a metalloamidase of the lipid A biosynthesis pathway. J. Bacteriol. 179 (1997) 2029-2037. [PMID: 9068651]
4. Wang, W., Maniar, M., Jain, R., Jacobs, J., Trias, J. and Yuan, Z. A fluorescence-based homogeneous assay for measuring activity of UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase. Anal. Biochem. 290 (2001) 338-346. [PMID: 11237337]
5. Whittington, D.A., Rusche, K.M., Shin, H., Fierke, C.A. and Christianson, D.W. Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 8146-8150. [PMID: 12819349]
6. Mochalkin, I., Knafels, J.D. and Lightle, S. Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor. Protein Sci. 17 (2008) 450-457. [PMID: 18287278]
Accepted name: N-methylcarbamate hydrolase
Reaction: an N-methyl carbamate ester + H2O = an alcohol + methylamine + CO2
Glossary: carbaryl = N-methyl-1-naphthyl carbamate
Other name(s): mcbA (gene name); cehA (gene name); cfdJ (gene name); carbaryl hydrolase; carbofuran hydrolase
Systematic name: N-methyl carbamate ester hydrolase
Comments: The enzyme catalyses the first step in the degradation of several carbamate insecticides such as carbaryl, carbofuran, isoprocarb, propoxur, aldicarb and oxamyl. It catalyses the cleavage of the ester bond to release N-methylcarbamate, which spontaneously hydrolyses to methylamine and CO2. The enzymes from several Gram-negative bacteria were shown to be located in the periplasm.
References:
1. Mulbry, W.W. and Eaton, R.W. Purification and characterization of the N-methylcarbamate hydrolase from Pseudomonas strain CRL-OK. Appl. Environ. Microbiol. 57 (1991) 3679-3682. [PMID: 1785941]
2. Hayatsu, M. and Nagata, T. Purification and characterization of carbaryl hydrolase from Blastobacter sp. strain M501. Appl. Environ. Microbiol. 59 (1993) 2121-2125. [PMID: 16348989]
3. Chapalmadugu, S. and Chaudhry, G.R. Isolation of a constitutively expressed enzyme for hydrolysis of carbaryl in Pseudomonas aeruginosa, J. Bacteriol. 175 (1993) 6711-6716. [PMID: 8407847]
4. Hayatsu, M., Mizutani, A., Hashimoto, M., Sato, K. and Hayano, K. Purification and characterization of carbaryl hydrolase from Arthrobacter sp. RC100. FEMS Microbiol. Lett. 201 (2001) 99-103. [PMID: 11445174]
5. Hashimoto, M., Fukui, M., Hayano, K. and Hayatsu, M. Nucleotide sequence and genetic structure of a novel carbaryl hydrolase gene (cehA) from Rhizobium sp. strain AC100. Appl. Environ. Microbiol. 68 (2002) 1220-1227. [PMID: 11872471]
6. Zhang, Q., Liu, Y. and Liu, Y.H. Purification and characterization of a novel carbaryl hydrolase from Aspergillus niger PY168. FEMS Microbiol. Lett. 228 (2003) 39-44. [PMID: 14612234]
7. Ozturk, B., Ghequire, M., Nguyen, T.P., De Mot, R., Wattiez, R. and Springael, D. Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene. Environ. Microbiol. 18 (2016) 4878-4887. [PMID: 27312345]
8. Kamini, Shetty, D., Trivedi, V.D., Varunjikar, M. and Phale, P.S. Compartmentalization of the carbaryl degradation pathway: molecular characterization of inducible periplasmic carbaryl hydrolase from Pseudomonas spp. Appl. Environ. Microbiol. 84 (2018) e02115-17 . [PMID: 29079626]
9. Yan, X., Jin, W., Wu, G., Jiang, W., Yang, Z., Ji, J., Qiu, J., He, J., Jiang, J. and Hong, Q. Hydrolase CehA and monooxygenase CfdC are responsible for carbofuran degradation in Sphingomonas sp. strain CDS-1. Appl. Environ. Microbiol. 84 (2018) . [PMID: 29884759]
10. Jiang, W., Gao, Q., Zhang, L., Wang, H., Zhang, M., Liu, X., Zhou, Y., Ke, Z., Wu, C., Qiu, J. and Hong, Q. Identification of the key amino acid sites of the carbofuran hydrolase CehA from a newly isolated carbofuran-degrading strain Sphingbium sp. CFD-1. Ecotoxicol Environ Saf 189 (2020) 109938. [PMID: 31759739]
Accepted name: UDP-2,3-diacylglucosamine diphosphatase
Reaction: a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-α-D-glucosamine + H2O = a lipid X + UMP
For diagram of reaction click here
Glossary: a lipid X = 2-N-[(3R)-3-hydroxyacyl]-3-O-[(3R)-3-hydroxyacyl]-α-D-glucosamine 1-phosphate =
2-N,3-O-bis[(3R)-3-hydroxyacyl]-α-D-glucosamine
Other name(s): lpxH (gene name); UDP-2,3-diacylglucosamine hydrolase; UDP-2,3-diacylglucosamine pyrophosphatase; ybbF (gene name); UDP-2,3-bis[(3R)-3-hydroxymyristoyl]-α-D-glucosamine 2,3-bis[(3R)-3-hydroxymyristoyl]-β-D-glucosaminyl 1-phosphate phosphohydrolase (incorrect); UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine 2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosaminyl 1-phosphate phosphohydrolase
Systematic name: UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-α-D-glucosamine 2-N,3-O-bis[(3R)-3-hydroxyacyl]-α-D-glucosamine-1-phosphate phosphohydrolase
Comments: The enzyme catalyses a step in the biosynthesis of lipid A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Babinski, K.J., Ribeiro, A.A. and Raetz, C.R. The Escherichia coli gene encoding the UDP-2,3-diacylglucosamine pyrophosphatase of lipid A biosynthesis. J. Biol. Chem. 277 (2002) 25937-25946. [PMID: 12000770]
2. Babinski, K.J., Kanjilal, S.J. and Raetz, C.R. Accumulation of the lipid A precursor UDP-2,3-diacylglucosamine in an Escherichia coli mutant lacking the lpxH gene. J. Biol. Chem. 277 (2002) 25947-25956. [PMID: 12000771]
3. Okada, C., Wakabayashi, H., Kobayashi, M., Shinoda, A., Tanaka, I. and Yao, M. Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa, Sci. Rep. 6 (2016) 32822. [PMID: 27609419]
4. Cho, J., Lee, C.J., Zhao, J., Young, H.E. and Zhou, P. Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis. Nat Microbiol 1 (2016) 16154. [PMID: 27780190]
5. Arenas, J., Pupo, E., de Jonge, E., Perez-Ortega, J., Schaarschmidt, J., van der Ley, P. and Tommassen, J. Substrate specificity of the pyrophosphohydrolase LpxH determines the asymmetry of Bordetella pertussis lipid A. J. Biol. Chem. 294 (2019) 7982-7989. [PMID: 30926608]
[EC 3.6.4.12 Transferred entry: DNA helicase. Now EC 5.6.2.3, DNA 5-3 helicase and EC 5.6.2.4, DNA 3-5 helicase (EC 3.6.4.12 created 2009, deleted 2021)]
[EC 3.7.1.27 Transferred entry: neryl diphosphate diphosphatase. Now EC 3.1.7.13, neryl diphosphate diphosphatase. (EC 3.7.1.27 created 2020, deleted 2021)]
Accepted name: difructose-dianhydride-III synthase
Reaction: inulobiose = α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride + H2O
Glossary: difructose anhydride III = α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride
inulobiose = β-D-fructofuranosyl-(2→1)-D-fructose
Other name(s): DFA-IIIase; difructose anhydride III hydrolase
Systematic name: inulobiose hydro-lyase (α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride-forming)
Comments: The enzyme participates in an inulin degradation pathway, in which it forms inulobiose from difructose anhydride III. A conformational change in the enzyme from the bacterium Pseudarthrobacter chlorophenolicus results in it also catalysing the activity of EC 4.2.2.18, inulin fructotransferase (DFA-III-forming).
References:
1. Tanaka, T., Uchiyama, T., Kobori, H. and Tanaka, K. Enzymic hydrolysis of di-D-fructofuranose 1, 2'; 2, 3' dianhydride with Arthrobacter ureafaciens, J. Biochem. 78 (1975) 1201-1206. [PMID: 1225919]
2. Neubauer, A., Walter, M., and Buchholz, K. Formation of inulobiose from difructoseanhydride III catalysed by a lysate from Arthrobacter ureafaciens ATCC 21124. Biocatalysis and Biotransformation 18 (2000) 443-455.
3. Saito, K., Sumita, Y., Nagasaka, Y., Tomita, F. and Yokota, A. Molecular cloning of the gene encoding the di-D-fructofuranose 1,2':2,3' dianhydride hydrolysis enzyme (DFA IIIase) from Arthrobacter sp. H65-7. J. Biosci. Bioeng. 95 (2003) 538-540. [PMID: 16233453]
4. Yu, S., Wang, X., Zhang, T., Stressler, T., Fischer, L., Jiang, B. and Mu, W. Identification of a novel di-D-fructofuranose 1,2':2,3' dianhydride (DFA III) hydrolysis enzyme from Arthrobacter aurescens SK8.001. PLoS One 10 (2015) e0142640. [PMID: 26555784]
5. Yu, S., Shen, H., Cheng, Y., Zhu, Y., Li, X., and Mu, W. Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue. ACS Catalysis 8 (2018) 10683-10697.
Accepted name: difructose-anhydride-I synthase
Reaction: inulobiose = bis-D-fructose 2',1:2,1'-dianhydride + H2O
Glossary: α-D-fructofuranose-β-D-fructofuranose 2',1:2,1'-dianhydride = bis-D-fructose 2',1:2,1'-dianhydride = difructose anhydride I = DFA-I
Other name(s): DFAIase; inulobiose hydrolase; bis-D-fructose 2',1:2,1'-dianhydride fructohydrolase
Systematic name: inulobiose hydro-lyase (α-D-fructofuranose-β-D-fructofuranose 2',1:2,1'-dianhydride-forming)
Comments: The enzyme, studied in the fungus Aspergillus fumigatus, may participate in an inulin degradation pathway in which it converts the product of EC 4.2.2.17, inulin fructotransferase (DFA-I-forming), to inulobiose, though in vitro activity was higher in the direction of DFA-I formation.
References:
1. Matsuyama, T. and Tanaka, K. On the enzyme of Aspergillus fumigatus producing difructose anhydride I from inulobiose. Agric. Biol. Chem. 53 (1989) 831-832.
2. Matsuyama, T., Tanaka, K., Mashiko, M. and Kanamoto, M. Enzymic formation of di-D-fructose 1,2'; 2,1' dianhydride from inulobiose by Aspergillus fumigatus, J. Biochem. (Tokyo) 92 (1982) 1325-1328. [PMID: 6757245]
Accepted name: nitrosuccinate lyase
Reaction: 2-nitrobutanedioate = fumarate + nitrite
Glossary: 2-nitrobutanedioate = nitrosuccinate
Other name(s): creD (gene name)
Systematic name: 2-nitrobutanedioate lyase (fumarate-forming)
Comments: The enzyme, found in some Actinobacteria, is involved in a pathway that forms nitrite, which is subsequently used to generate a diazo group in some secondary metabolites.
References:
1. Sugai, Y., Katsuyama, Y. and Ohnishi, Y. A nitrous acid biosynthetic pathway for diazo group formation in bacteria. Nat. Chem. Biol. 12 (2016) 73-75. [PMID: 26689788]
2. Hagihara, R., Katsuyama, Y., Sugai, Y., Onaka, H. and Ohnishi, Y. Novel desferrioxamine derivatives synthesized using the secondary metabolism-specific nitrous acid biosynthetic pathway in Streptomyces davawensis, J. Antibiot. (Tokyo) 71 (2018) 911-919. [PMID: 30120394]
Accepted name: L-piperazate synthase
Reaction: N5-hydroxy-L-ornithine = (3S)-1,2-diazinane-3-carboxylate + H2O
Glossary: (3S)-1,2-diazinane-3-carboxylate = (3S)-pyridazin-3-carboxylate = L-piperazate
Other name(s): ktzT (gene name)
Systematic name: (3S)-1,2-diazinane-3-carboxylate hydrolase (N5-hydroxy-L-ornithine-forming)
Comments: Contains a heme b cofactor. The enzyme, characterized from the bacterium Kutzneria sp. 744, is one of very few enzymes known to result in the formation of an N-N bond. (3S)-1,2-diazinane-3-carboxylate (piperazate) is known to be incorporated into assorted secondary products that are produced by nonribosomal peptide synthetase or nonribosomal peptide synthetase/polyketide synthase hybrid pathways, such as the kutznerides, padanamides, himastatins, and sanglifehrins.
References:
1. Du, Y.L., He, H.Y., Higgins, M.A. and Ryan, K.S. A heme-dependent enzyme forms the nitrogen-nitrogen bond in piperazate. Nat. Chem. Biol. 13 (2017) 836-838. [PMID: 28628093]
Accepted name: aliphatic aldoxime dehydratase
Reaction: an aliphatic aldoxime = an aliphatic nitrile + H2O
Other name(s): OxdA; aliphatic aldoxime hydro-lyase
Systematic name: aliphatic aldoxime hydro-lyase (aliphatic-nitrile-forming)
Comments: The enzyme from Pseudomonas chlororaphis contains Ca2+ and protoheme IX, the iron of which must be in the form Fe(II) for activity. The enzyme exhibits a strong preference for aliphatic aldoximes, such as butyraldoxime and acetaldoxime, over aromatic aldoximes, such as pyridine-2-aldoxime, which is a poor substrate. No activity was found with the aromatic aldoximes benzaldoxime and pyridine-4-aldoxime.
References:
1. Oinuma, K.-I., Hashimoto, Y., Konishi, K., Goda, M., Noguchi, T., Higashibata, H. and Kobayashi, M. Novel aldoxime dehydratase involved in carbon-nitrogen triple bond synthesis of Pseudomonas chlororaphis B23: Sequencing, gene expression, purification and characterization. J. Biol. Chem. 278 (2003) 29600-29608. [PMID: 12773527]
2. Xie, S.X., Kato, Y., Komeda, H., Yoshida, S. and Asano, Y. A gene cluster responsible for alkylaldoxime metabolism coexisting with nitrile hydratase and amidase in Rhodococcus globerulus A-4. Biochemistry 42 (2003) 12056-12066. [PMID: 14556637]
3. Kato, Y., Yoshida, S., Xie, S.-X. and Asano, Y. Aldoxime dehydratase co-existing with nitrile hydratase and amidase in the iron-type nitrile hydratase-producer Rhodococcus sp. N-771. J. Biosci. Bioeng. 97 (2004) 250-259. [PMID: 16233624]
Accepted name: indoleacetaldoxime dehydratase
Reaction: (indol-3-yl)acetaldehyde oxime = (indol-3-yl)acetonitrile + H2O
For diagram of reaction, click here
Other name(s): indoleacetaldoxime hydro-lyase; 3-indoleacetaldoxime hydro-lyase; indole-3-acetaldoxime hydro-lyase; indole-3-acetaldehyde-oxime hydro-lyase; (indol-3-yl)acetaldehyde-oxime hydro-lyase
Systematic name: (indol-3-yl)acetaldehyde-oxime hydro-lyase [(indol-3-yl)acetonitrile-forming]
References:
1. Kumar, S.A. and Mahadevan, S. 3-Indoleacetaldoxime hydro-lyase: a pyridoxal-5'-phosphate activated enzyme. Arch. Biochem. Biophys. 103 (1963) 516-518. [PMID: 14099566]
2. Mahadevan, S. Conversion of 3-indoleacetoxime to 3-indoleacetonitrile by plants. Arch. Biochem. Biophys. 100 (1963) 557-558.
Accepted name: phenylacetaldoxime dehydratase
Reaction: (Z)-phenylacetaldehyde oxime = phenylacetonitrile + H2O
For diagram of reaction, click here
Other name(s): PAOx dehydratase; arylacetaldoxime dehydratase; OxdB; (Z)-phenylacetaldehyde-oxime hydro-lyase
Systematic name: (Z)-phenylacetaldehyde-oxime hydro-lyase (phenylacetonitrile-forming)
Comments: The enzyme from Bacillus sp. OxB-1 contains protoheme IX, the iron of which must be in the form iron(II) for activity. (Z)-Phenylacetaldoxime binds to ferric heme (the iron(III) form) via the oxygen atom whereas it binds to the active ferrous form via the nitrogen atom. In this way, the oxidation state of the heme controls the coordination stucture of the substrate—heme complex, which regulates enzyme activity [2]. The enzyme is active towards several (Z)-arylacetaldoximes and (E/Z)-alkylaldoximes as well as towards arylalkylaldoximes such as 3-phenylpropionaldoxime and 4-phenylbutyraldoxime. However, it is inactive with phenylacetaldoximes that have a substituent group at an α-site of an oxime group, for example, with (E/Z)-2-phenylpropionaldoxime and (E/Z)-mandelaldoxime. The activity of the enzyme is inhibited completely by the heavy-metal cations Cu+, Cu2+, Ag+ and Hg+ whereas Fe2+ and Sn2+ have an activatory effect.
References:
1. Kato, Y., Nakamura, K., Sakiyama, H., Mayhew, S.G. and Asano, Y. Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Biochemistry 39 (2000) 800-809. [PMID: 10651646]
2. Kobayashi, K., Yoshioka, S., Kato, Y., Asano, Y. and Aono, S. Regulation of aldoxime dehydratase activity by redox-dependent change in the coordination structure of the aldoxime-heme complex. J. Biol. Chem. 280 (2005) 5486-5490. [PMID: 15596434]
EC 4.98 ATP-independent chelatases
EC 4.98.1 Forming coordination complexes
Accepted name: protoporphyrin ferrochelatase
Reaction: protoheme + 2 H+ = protoporphyrin + Fe2+
For diagram of reaction click here
Other name(s): ferro-protoporphyrin chelatase; iron chelatase (ambiguous); heme synthetase (ambiguous); heme synthase (ambiguous); protoheme ferro-lyase; ferrochelatase (ambiguous)
Systematic name: protoheme ferro-lyase (protoporphyrin-forming)
Comments: The enzyme catalyses the terminal step in the heme biosynthesis pathways of eukaryotes and Gram-negative bacteria. The reaction is catalysed only in the reverse direction.
References:
1. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 1. Assay and properties of ferrochelatase from a pig-liver mitochondrial extract. Biochem. J. 87 (1963) 181-185. [PMID: 13972328]
2. Porra, R.J. and Jones, O.T. Studies on ferrochelatase. 2. An investigation of the role of ferrochelatase in the biosynthesis of various haem prosthetic groups. Biochem. J. 87 (1963) 186-192. [PMID: 13972329]
3. Bloomer, J.R., Hill, H.D., Morton, K.O., Anderson-Burnham, L.A. and Straka, J.G. The enzyme defect in bovine protoporphyria. Studies with purified ferrochelatase. J. Biol. Chem. 262 (1987) 667-671. [PMID: 3805002]
[EC 4.99.1.1 Transferred entry: protoporphyrin ferrochelatase, now classified as EC 4.98.1.1, protoporphyrin ferrochelatase (EC 4.99.1.1 created 1965, modified 2016, deleted 2021)]
[EC 4.99.1.5 Transferred entry: aliphatic aldoxime dehydratase, now classified as EC 4.8.1.2, aliphatic aldoxime dehydratase (EC 4.99.1.5 created 2004, deleted 2021)]
[EC 4.99.1.6 Transferred entry: indoleacetaldoxime dehydratase, now classified as EC 4.8.1.3, indoleacetaldoxime dehydratase (EC 4.99.1.6 created 1965 as EC 4.2.1.29, transferred 2004 to EC 4.99.1.6, deleted 2021)]
[EC 4.99.1.7 Transferred entry: phenylacetaldoxime dehydratase, now classified as EC 4.8.1.4, phenylacetaldoxime dehydratase (EC 4.99.1.7 created 2005, deleted 2021)]
Accepted name: glucose-6-phosphate isomerase
Reaction: α-D-glucose 6-phosphate = β-D-fructofuranose 6-phosphate
For diagram of reaction click here, another example click here, another example click here another example click here
Other name(s): phosphohexose isomerase; phosphohexomutase; oxoisomerase; hexosephosphate isomerase; phosphosaccharomutase; phosphoglucoisomerase; phosphohexoisomerase; phosphoglucose isomerase; glucose phosphate isomerase; hexose phosphate isomerase; D-glucose-6-phosphate ketol-isomerase
Systematic name: α-D-glucose-6-phosphate aldose-ketose-isomerase (configuration-inverting)
Comments: The enzyme from yeast catalyses the reversible conversion specifically between the α-D-glucose 6-phosphate and β-D-fructofuranose 6-phosphate. The enzyme also catalyses the anomerization of both D-hexose 6-phosphates [7].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9001-41-6
References:
1. Ramasarma, T. and Giri, K.V. Phosphoglucose isomerase of green gram (Phaseolus radiatus). Arch. Biochem. Biophys. 62 (1956) 91-96. [PMID: 13314642]
2. Tsuboi, K.K., Estrada, J. and Hudson, P.B. Enzymes of the human erythrocytes. IV. Phosphoglucose isomerase, purification and properties. J. Biol. Chem. 231 (1958) 19-29. [PMID: 13538944]
3. Noltmann, E. and Bruns, F.H. Reindarstellung und Eigenschaften von Phosphoglucose-isomerase aus Hefe. Biochem. Z. 331 (1959) 436-445.
4. Baich, A., Wolfe, R.G. and Reithel, F.J. The enzymes of mammary gland. I. Isolation of phosphoglucose isomerase. J. Biol. Chem. 235 (1960) 3130-3133. [PMID: 13685918]
5. Noltmann, E.A. Isolation of crystalline phosphoglucose isomerase from rabbit muscle. J. Biol. Chem. 239 (1964) 1545-1550. [PMID: 14189891]
6. Nakagawa, Y. and Noltmann, E.A. Isolation of crystalline phosphoglucose isomerase from brewers' yeast. J. Biol. Chem. 240 (1965) 1877-1881. [PMID: 14299604]
7. Willem, R., Biesemans, M., Hallenga, K., Lippens, G., Malaisse-Lagae, F. and Malaisse, W.J. Dual anomeric specificity and dual anomerase activity of phosphoglucoisomerase quantified by two-dimensional phase-sensitive 13C EXSY NMR. J. Biol. Chem. 267 (1992) 210-217. [PMID: 1730590]
Accepted name: lachrymatory-factor synthase
Reaction: (E)-alk-1-en-1-SO-peroxol = (Z)-alkanethial oxide
Glossary: alk-1-en-1-SO-peroxol = S-alk-1-en-1-ylthiohydroperoxide
alkanethial oxide = alkylidene-λ4-sulfanone = (alkylidenesulfaniumyl)oxidanide
Other name(s): LFS
Systematic name: (E)-alk-1-en-1-SO-peroxol isomerase [(Z)-alkanethial S-oxide-forming]
Comments: The enzyme is responsible for production of the irritating lachrymatory factor that is released by onions and related species when they are chopped. It acts of the product of EC 4.4.1.4, alliin lyase. The enzyme from Allium cepa (onion) acts on (E)-prop-1-en-1-SO-peroxol and produces (Z)-propanethial oxide, while the enzyme from Allium siculum (honey garlic) acts on (E)-but-1-en-1-SO-peroxol and produces (Z)-butanethial oxide.
References:
1. Norris, P.G., Nunn, A.V., Hawk, J.L. and Cox, T.M. Genetic heterogeneity in erythropoietic protoporphyria: a study of the enzymatic defect in nine affected families. J. Invest. Dermatol. 95 (1990) 260-263. [PMID: 2384686]
2. Imai, S., Tsuge, N., Tomotake, M., Nagatome, Y., Sawada, H., Nagata, T. and Kumagai, H. Plant biochemistry: an onion enzyme that makes the eyes water. Nature 419 (2002) 685. [PMID: 12384686]
3. Eady, C.C., Kamoi, T., Kato, M., Porter, N.G., Davis, S., Shaw, M., Kamoi, A. and Imai, S. Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile. Plant Physiol. 147 (2008) 2096-2106. [PMID: 18583530]
4. Kubec, R., Cody, R.B., Dane, A.J., Musah, R.A., Schraml, J., Vattekkatte, A. and Block, E. Applications of direct analysis in real time-mass spectrometry (DART-MS) in Allium chemistry. (Z)-butanethial S-oxide and 1-butenyl thiosulfinates and their S-(E)-1-butenylcysteine S-oxide precursor from Allium siculum. J. Agric. Food Chem. 58 (2010) 1121-1128. [PMID: 20047275]
Accepted name: DNA 5'-3' helicase
Reaction: Couples ATP hydroysis with the unwinding of duplex DNA at the replication fork by translocating in the 5'-3' direction. This creates two antiparallel DNA single strands (ssDNA). The leading ssDNA polymer is the template for DNA polymerase III holoenzyme which synthesizes a continuous strand.
Other name(s): DnaB helicase; replication fork helicase; 5' to 3' DNA helicase; BACH1 helicase; BcMCM; BLM protein; BRCA1-associated C-terminal helicase; CeWRN-1; Dbp9p; DNA helicase A; DNA helicase E; DNA helicase II; DNA helicase III; DNA helicase VI; dnaB (gene name); DnaB helicase E1; helicase HDH IV; Hel E; helicase DnaB; helicase domain of bacteriophage T7 gene 4 protein helicase; PcrA helicase; hHcsA; Hmi1p; hPif1; MCM helicase; MCM protein; MPH1; PcrA; PfDH A; Pfh1p; PIF1; replicative DNA helicase
Systematic name: DNA 5'-3' helicase (ATP-hydrolysing)
Comments: The activity is stimulated by DNA polymerase III. As the lagging ssDNA is created, it becomes coated with S Single-Stranded DNA Binding protein (SSB). Once every 500-2000 nucleotides, primase is stimulated by DnaB helicase to synthesize a primer at the replication fork. This primer is elongated by the lagging strand half of DNA polymerase III holoenzyme.
References:
1. Lohman, T.M. Helicase-catalyzed DNA unwinding. J. Biol. Chem. 268 (1993) 2269-2272. [PMID: 8381400]
2. Jezewska, M.J. and Bujalowski, W. Global conformational transitions in Escherichia coli primary replicative helicase DnaB protein induced by ATP, ADP, and single-stranded DNA binding. Multiple conformational states of the helicase hexamer. J. Biol. Chem. 271 (1996) 4261-4265. [PMID: 8626772]
3. Ivessa, A.S., Zhou, J.Q., Schulz, V.P., Monson, E.K. and Zakian, V.A. Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. Genes Dev. 16 (2002) 1383-1396. [PMID: 12050116]
4. Zhou, J.Q., Qi, H., Schulz, V.P., Mateyak, M.K., Monson, E.K. and Zakian, V.A. Schizosaccharomyces pombe pfh1+ encodes an essential 5' to 3' DNA helicase that is a member of the PIF1 subfamily of DNA helicases. Mol. Biol. Cell 13 (2002) 2180-2191. [PMID: 12058079]
5. Ivanov, K.A. and Ziebuhr, J. Human coronavirus 229E nonstructural protein 13: characterization of duplex-unwinding, nucleoside triphosphatase, and RNA 5'-triphosphatase activities. J. Virol. 78 (2004) 7833-7838. [PMID: 15220459]
6. Toseland, C.P. and Webb, M.R. ATPase mechanism of the 5'-3' DNA helicase, RecD2: evidence for a pre-hydrolysis conformation change. J. Biol. Chem. 288 (2013) 25183-25193. [PMID: 23839989]
Accepted name: DNA 3'-5' helicase
Reaction: Couples ATP hydroysis with the unwinding of duplex DNA by translocating in the 3'-5' direction.
Other name(s): uvrD (gene name); rep (gene name); RECQ (gene name); MER3 (gene name); Holliday junction DNA helicase
Systematic name: DNA 3'-5' helicase (ATP-hydrolysing)
Comments: Helicases are motor proteins that can transiently catalyse the unwinding of energetically stable duplex DNA or RNA molecules by using ATP hydrolysis as the source of energy (although other nucleoside triphosphates can replace ATP in some cases). DNA helicases unwind duplex DNA and are involved in replication, repair, recombination, transcription, pre-rRNA processing, and translation initiation. Mechanistically, DNA helicases are divided into those that can translocate in the 3'-5' direction and those that translocate in the 5'-3' direction with respect to the strand on which they initially bind. This entry describes a number of DNA helicases that translocate in the 3'-5' direction. Many of the enzymes require a 3' single-stranded DNA tail. The Rep protein is a component of the bacterial replisome, providing a replication fork-specific motor. The UvrD enzyme, found in Gram-negative bacteria, is involved in maintenance of chromosomal integrity. The RecQ proteins are a family of eukaryotic helicases that are involved in DNA replication, transcription and repair. The Mer3 helicase, found in fungi and plants, is required for crossover formation during meiosis. cf. EC 5.6.2.3, DNA 5'-3' helicase.
References:
1. Takahashi, S., Hours, C., Chu, A. and Denhardt, D.T. The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can. J. Biochem. 57 (1979) 855-866. [PMID: 383240]
2. Nakagawa, T., Flores-Rozas, H. and Kolodner, R.D. The MER3 helicase involved in meiotic crossing over is stimulated by single-stranded DNA-binding proteins and unwinds DNA in the 3' to 5' direction. J. Biol. Chem. 276 (2001) 31487-31493. [PMID: 11376001]
3. Ozsoy, A.Z., Sekelsky, J.J. and Matson, S.W. Biochemical characterization of the small isoform of Drosophila melanogaster RECQ5 helicase. Nucleic Acids Res. 29 (2001) 2986-2993. [PMID: 11452023]
4. Curti, E., Smerdon, S.J. and Davis, E.O. Characterization of the helicase activity and substrate specificity of Mycobacterium tuberculosis UvrD. J. Bacteriol. 189 (2007) 1542-1555. [PMID: 17158674]
Accepted name: tubulin-glutamate ligase
Reaction: n ATP + [tubulin]-L-glutamate + n L-glutamate = [tubulin]-(γ-(poly-α-L-glutamyl)-L-glutamyl)-L-glutamate + n ADP + n phosphate (overall reaction)
(1a) ATP + [tubulin]-L-glutamate + L-glutamate = [tubulin]-(γ-L-glutamyl)-L-glutamate + ADP + phosphate
(1b) ATP + [tubulin]-(γ-L-glutamyl)-L-glutamate + L-glutamate = [tubulin]-(α-L-glutamyl-γ-L-glutamyl)-L-glutamate + ADP + phosphate
(1c) ATP + [tubulin]-(α-L-glutamyl-γ-L-glutamyl)-L-glutamate + n L-glutamate = [tubulin]-(γ-(poly-α-L-glutamyl)-L-glutamyl)-L-glutamate + n ADP + n phosphate
Other name(s): α-tubulin-glutamate ligase; tubulin polyglutamylase; TTLL1 (ambiguous); TTLL5 (ambiguous); TTLL6 (ambiguous)
Systematic name: [tubulin]-L-glutamate:L-glutamate ligase (ADP-forming)
Comments: The eukaryotic tubulin proteins, which polymerize into microtubules, are highly modified by the addition of side-chains. The polyglutamylation reaction catalysed by this group of enzymes consists of two biochemically distinct steps: initiation and elongation. Initiation comprises the formation of an isopeptide bond with the γ-carboxyl group of the glutamate acceptor site in a glutamate-rich C-terminal region of tubulin, whereas elongation consists of the addition of glutamate residues linked by regular peptide bonds to the γ-linked residue. This entry describes enzymes that act on both α- and β-tubulins.
References:
1. Regnard, C., Audebert, S., Desbruyeres, Denoulet, P. and Edde, B. Tubulin polyglutamylase: partial purification and enzymatic properties. Biochemistry 37 (1998) 8395-8404. [PMID: 9622491]
2. Regnard, C., Desbruyeres, E., Denoulet, P. and Edde, B. Tubulin polyglutamylase: isozymic variants and regulation during the cell cycle in HeLa cells. J. Cell Sci. 112 (1999) 4281-4289. [PMID: 10564646]
3. Westermann, S., Plessmann, U. and Weber, K. Synthetic peptides identify the minimal substrate requirements of tubulin polyglutamylase in side chain elongation. FEBS Lett. 459 (1999) 90-94. [PMID: 10508923]
4. Janke, C., Rogowski, K., Wloga, D., Regnard, C., Kajava, A.V., Strub, J.M., Temurak, N., van Dijk, J., Boucher, D., van Dorsselaer, A., Suryavanshi, S., Gaertig, J. and Edde, B. Tubulin polyglutamylase enzymes are members of the TTL domain protein family. Science 308 (2005) 1758-1762. [PMID: 15890843]
5. van Dijk, J., Rogowski, K., Miro, J., Lacroix, B., Edde, B. and Janke, C. A targeted multienzyme mechanism for selective microtubule polyglutamylation. Mol. Cell 26 (2007) 437-448. [PMID: 17499049]
6. Wloga, D., Rogowski, K., Sharma, N., Van Dijk, J., Janke, C., Edde, B., Bre, M.H., Levilliers, N., Redeker, V., Duan, J., Gorovsky, M.A., Jerka-Dziadosz, M. and Gaertig, J. Glutamylation on α-tubulin is not essential but affects the assembly and functions of a subset of microtubules in Tetrahymena thermophila, Eukaryot Cell 7 (2008) 1362-1372. [PMID: 18586949]
7. van Dijk, J., Miro, J., Strub, J.M., Lacroix, B., van Dorsselaer, A., Edde, B. and Janke, C. Polyglutamylation is a post-translational modification with a broad range of substrates. J. Biol. Chem. 283 (2008) 3915-3922. [PMID: 18045879]
Accepted name: β-tubulin-glutamate ligase
Reaction: n ATP + [β-tubulin]-L-glutamate + n L-glutamate = [β-tubulin]-(γ-(poly-α-L-glutamyl)-L-glutamyl)-L-glutamate + n ADP + n phosphate (overall reaction)
(1a) ATP + [β-tubulin]-L-glutamate + L-glutamate = [β-tubulin]-(γ-L-glutamyl)-L-glutamate + ADP + phosphate
(1b) ATP + [β-tubulin]-(γ-L-glutamyl)-L-glutamate + L-glutamate = [β-tubulin]-(α-L-glutamyl-γ-L-glutamyl)-L-glutamate + ADP + phosphate
(1c) ATP + [β-tubulin]-(α-L-glutamyl-γ-L-glutamyl)-L-glutamate + n L-glutamate = [β-tubulin]-(γ-(poly-α-L-glutamyl)-L-glutamyl)-L-glutamate + n ADP + n phosphate
Other name(s): β-tubulin polyglutamylase; TTLL4 (ambiguous); TTLL7 (ambiguous)
Systematic name: [β-tubulin]-L-glutamate:L-glutamate ligase (ADP-forming)
Comments: The eukaryotic tubulin proteins, which polymerize into microtubules, are highly modified by the addition of side-chains. The polyglutamylation reaction catalysed by this group of enzymes consists of two biochemically distinct steps: initiation and elongation. Initiation comprises the formation of an isopeptide bond with the γ-carboxyl group of the glutamate acceptor site, whereas elongation consists of the addition of glutamate residues linked by regular peptide bonds to the γ-linked residue. This entry describes enzymes that act on β-tubulins and other proteins with glutamate-rich regions but not on α-tubulins.
References:
1. Regnard, C., Audebert, S., Desbruyeres, Denoulet, P. and Edde, B. Tubulin polyglutamylase: partial purification and enzymatic properties. Biochemistry 37 (1998) 8395-8404. [PMID: 9622491]
2. Regnard, C., Desbruyeres, E., Denoulet, P. and Edde, B. Tubulin polyglutamylase: isozymic variants and regulation during the cell cycle in HeLa cells. J. Cell Sci. 112 (1999) 4281-4289. [PMID: 10564646]
3. Ikegami, K., Mukai, M., Tsuchida, J., Heier, R.L., Macgregor, G.R. and Setou, M. TTLL7 is a mammalian β-tubulin polyglutamylase required for growth of MAP2-positive neurites. J. Biol. Chem. 281 (2006) 30707-30716. [PMID: 16901895]
4. van Dijk, J., Miro, J., Strub, J.M., Lacroix, B., van Dorsselaer, A., Edde, B. and Janke, C. Polyglutamylation is a post-translational modification with a broad range of substrates. J. Biol. Chem. 283 (2008) 3915-3922. [PMID: 18045879]
EC 6.7 Forming nitrogen-nitrogen bonds
Accepted name: 3-amino-2-hydroxy-4-methoxybenzoate diazotase
Reaction: ATP + 3-amino-2-hydroxy-4-methoxybenzoate + nitrite = AMP + diphosphate + cremeomycin + H2O
For diagram of reaction, click here
Glossary: cremeomycin = 6-carboxy-2-diazonio-3-methoxyphenolate
Other name(s): creM (gene name)
Systematic name: 3-amino-2-hydroxy-4-methoxybenzoate:nitrite ligase (AMP-forming)
Comments: The enzyme, characterized from Streptomyces cremeus, catalyses the last step in the biosynthesis of the ortho-diazoquinone cremeomycin.
References:
1. Waldman, A.J. and Balskus, E.P. Discovery of a diazo-forming enzyme in cremeomycin biosynthesis. J. Org. Chem. 83 (2018) 7539-7546. [PMID: 29771512]