The Enzyme Database

Displaying entries 151-200 of 262.

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EC 6.3.2.20     
Accepted name: indoleacetate—lysine synthetase
Reaction: ATP + (indol-3-yl)acetate + L-lysine = ADP + phosphate + N6-[(indol-3-yl)acetyl]-L-lysine
Other name(s): indoleacetate:L-lysine ligase (ADP-forming)
Systematic name: (indol-3-yl)acetate:L-lysine ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 103537-15-1
References:
1.  Glass, N.L. and Kosuge, T. Cloning of the gene for indoleacetic acid-lysine synthetase from Pseudomonas syringae subsp. savastanoi. J. Bacteriol. 166 (1986) 598. [DOI] [PMID: 3084452]
2.  Hutzinger, O. and Kosuge, T. Microbial synthesis and degradation of indole-3-acetic acid. 3. The isolation and characterization of indole-3-acetyl-ε-L-lysine. Biochemistry 7 (1968) 601–605. [PMID: 5644130]
[EC 6.3.2.20 created 1989]
 
 
EC 6.3.2.21      
Deleted entry: ubiquitin—calmodulin ligase. The reaction is performed by the sequential action of EC 6.2.1.45 (ubiquitin-activating enzyme E1), several ubiquitin transferases and finally by EC 2.3.2.27 [ubiquitin transferase RING E3 (calmodulin-selective)]
[EC 6.3.2.21 created 1990, deleted 2015]
 
 
EC 6.3.2.22      
Transferred entry: diphthine—ammonia ligase. Now EC 6.3.1.14, diphthine—ammonia ligase.
[EC 6.3.2.22 created 1990, deleted 2010]
 
 
EC 6.3.2.23     
Accepted name: homoglutathione synthase
Reaction: ATP + γ-L-glutamyl-L-cysteine + β-alanine = ADP + phosphate + γ-L-glutamyl-L-cysteinyl-β-alanine
Other name(s): homoglutathione synthetase; β-alanine specific hGSH synthetase
Systematic name: γ-L-glutamyl-L-cysteine:β-alanine ligase (ADP-forming)
Comments: Not identical with EC 6.3.2.3 glutathione synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 113875-72-2
References:
1.  Macnicol, P.K. Homoglutathione and glutathione synthetases of legume seedlings - partial-purification and substrate-specificity. Plant Sci. 53 (1987) 229–235.
[EC 6.3.2.23 created 1990]
 
 
EC 6.3.2.24     
Accepted name: tyrosine—arginine ligase
Reaction: ATP + L-tyrosine + L-arginine = AMP + diphosphate + L-tyrosyl-L-arginine
Other name(s): tyrosyl-arginine synthase; kyotorphin synthase; kyotorphin-synthesizing enzyme; kyotorphin synthetase
Systematic name: L-tyrosine:L-arginine ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 116036-78-3
References:
1.  Ueda, H., Yoshihara, Y., Fukushima, N., Shiomi, H., Nakamura, A. and Takagi, H. Kyotorphin (tyrosine-arginine) synthetase in rat brain synaptosomes. J. Biol. Chem. 262 (1987) 8165–8173. [PMID: 3597366]
[EC 6.3.2.24 created 1992]
 
 
EC 6.3.2.25     
Accepted name: tubulin—tyrosine ligase
Reaction: ATP + detyrosinated α-tubulin + L-tyrosine = α-tubulin + ADP + phosphate
Systematic name: α-tubulin:L-tyrosine ligase (ADP-forming)
Comments: L-Tyrosine is linked via a peptide bond to the C-terminus of de-tyrosinated α-tubulin (des-Tyrω-α-tubulin). The enzyme is highly specific for α-tubulin and moderately specific for ATP and L-tyrosine. L-Phenylalanine and 3,4-dihydroxy-L-phenylalanine are transferred but with higher Km values.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 60321-03-1
References:
1.  Wehland, J., Schröder, H.C., Weber, K. Isolation and purification of tubulin-tyrosine ligase. Methods Enzymol. 134 (1986) 170–179. [PMID: 3821560]
2.  Rudiger, M., Wehland, J., Weber, K. The carboxy-terminal peptide of detyrosinated α tubulin provides a minimal system to study the substrate specificity of tubulin-tyrosine ligase. Eur. J. Biochem. 220 (1994) 309–320. [DOI] [PMID: 7510228]
[EC 6.3.2.25 created 1999]
 
 
EC 6.3.2.26     
Accepted name: N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase
Reaction: 3 ATP + L-2-aminohexanedioate + L-cysteine + L-valine + H2O = 3 AMP + 3 diphosphate + N-[L-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine
For diagram of penicillin-N and deacetoxycephalosporin-C biosynthesis, click here and for possible mechanism of reaction, click here
Other name(s): L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase; ACV synthetase; L-α-aminoadipyl-cysteinyl-valine synthetase;
Systematic name: L-2-aminohexanedioate:L-cysteine:L-valine ligase (AMP-forming, valine-inverting)
Comments: Requires Mg2+. The enzyme contains 4′-phosphopantetheine, which may be involved in the mechanism of the reaction. Forms part of the penicillin biosynthesis pathway (for pathway, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57219-73-5
References:
1.  Byford, M.F., Baldwin, J.E., Shiau, C.-Y. and Schofield, C.J. The mechanism of ACV synthetase. Chem. Rev. 97 (1997) 2631–2649. [DOI] [PMID: 11851475]
2.  Theilgaard, H.B., Kristiansen, K.N., Henriksen, C.M. and Nielsen, J. Purification and characterization of δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine synthetase from Penicillium chrysogenum. Biochem. J. 327 (1997) 185–191. [PMID: 9355751]
[EC 6.3.2.26 created 2002]
 
 
EC 6.3.2.27      
Deleted entry: The activity is covered by two independent enzymes, EC 6.3.2.38 N2-citryl-N6-acetyl-N6-hydroxylysine synthase, and EC 6.3.2.39, aerobactin synthase
[EC 6.3.2.27 created 2002, modified 2006, deleted 2012]
 
 
EC 6.3.2.28      
Transferred entry: L-amino-acid α-ligase. Now EC 6.3.2.49, L-alanine-L-anticapsin ligase
[EC 6.3.2.28 created 2006, deleted 2015]
 
 
EC 6.3.2.29     
Accepted name: cyanophycin synthase (L-aspartate-adding)
Reaction: ATP + [L-Asp(4-L-Arg)]n + L-Asp = ADP + phosphate + [L-Asp(4-L-Arg)]n-L-Asp
For diagram of cyanophycin biosynthesis, click here
Glossary: cyanophycin = [L-Asp(4-L-Arg)]n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]n = poly{N4-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}
Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)
Systematic name: cyanophycin:L-aspartate ligase (ADP-forming)
Comments: Requires Mg2+ for activity. Both this enzyme and EC 6.3.2.30, cyanophycin synthase (L-arginine-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2,4]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 131554-17-1
References:
1.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297–306. [PMID: 11131019]
2.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176–2182. [DOI] [PMID: 11319097]
3.  Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687–693. [PMID: 6767688]
4.  Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561–5570. [DOI] [PMID: 10951215]
5.  Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522–529. [PMID: 12132696]
6.  Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154–159. [DOI] [PMID: 9652408]
[EC 6.3.2.29 created 2007]
 
 
EC 6.3.2.30     
Accepted name: cyanophycin synthase (L-arginine-adding)
Reaction: ATP + [L-Asp(4-L-Arg)]n-L-Asp + L-Arg = ADP + phosphate + [L-Asp(4-L-Arg)]n+1
For diagram of cyanophycin biosynthesis, click here
Glossary: cyanophycin = [L-Asp(4-L-Arg)]n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]n = poly{N4-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}
Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)
Systematic name: cyanophycin:L-arginine ligase (ADP-forming)
Comments: Requires Mg2+ for activity. Both this enzyme and EC 6.3.2.29, cyanophycin synthase (L-aspartate-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2,4]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2]. Canavanine and lysine can be incoporated into the polymer instead of arginine [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 131554-17-1
References:
1.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297–306. [PMID: 11131019]
2.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176–2182. [DOI] [PMID: 11319097]
3.  Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687–693. [PMID: 6767688]
4.  Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561–5570. [DOI] [PMID: 10951215]
5.  Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522–529. [PMID: 12132696]
6.  Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154–159. [DOI] [PMID: 9652408]
[EC 6.3.2.30 created 2007]
 
 
EC 6.3.2.31     
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor F420 (coenzyme F420) by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.31 created 2010]
 
 
EC 6.3.2.32     
Accepted name: coenzyme γ-F420-2:α-L-glutamate ligase
Reaction: ATP + coenzyme γ-F420-2 + L-glutamate = ADP + phosphate + coenzyme α-F420-3
For diagram of coenzyme F420 biosynthesis, click here
Other name(s): MJ1001; CofF protein; γ-F420-2:α-L-glutamate ligase
Systematic name: L-glutamate:coenzyme γ-F420-2 (ADP-forming)
Comments: The enzyme caps the γ-glutamyl tail of the hydride carrier coenzyme F420 [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Li, H., Xu, H., Graham, D.E. and White, R.H. Glutathione synthetase homologs encode α-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses. Proc. Natl. Acad. Sci. USA 100 (2003) 9785–9790. [DOI] [PMID: 12909715]
[EC 6.3.2.32 created 2010]
 
 
EC 6.3.2.33     
Accepted name: tetrahydrosarcinapterin synthase
Reaction: ATP + tetrahydromethanopterin + L-glutamate = ADP + phosphate + 5,6,7,8-tetrahydrosarcinapterin
For diagram of methanopterin biosynthesis (part 4), click here
Other name(s): H4MPT:α-L-glutamate ligase; MJ0620; MptN protein
Systematic name: tetrahydromethanopterin:α-L-glutamate ligase (ADP-forming)
Comments: This enzyme catalyses the biosynthesis of 5,6,7,8-tetrahydrosarcinapterin, a modified form of tetrahydromethanopterin found in the Methanosarcinales. It does not require K+, and does not discriminate between ATP and GTP [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Li, H., Xu, H., Graham, D.E. and White, R.H. Glutathione synthetase homologs encode α-L-glutamate ligases for methanogenic coenzyme F420 and tetrahydrosarcinapterin biosyntheses. Proc. Natl. Acad. Sci. USA 100 (2003) 9785–9790. [DOI] [PMID: 12909715]
[EC 6.3.2.33 created 2010]
 
 
EC 6.3.2.34     
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor 420 (coenzyme F420) by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.34 created 2010, modified 2023]
 
 
EC 6.3.2.35     
Accepted name: D-alanine—D-serine ligase
Reaction: D-alanine + D-serine + ATP = D-alanyl-D-serine + ADP + phosphate
Other name(s): VanC; VanE; VanG
Systematic name: D-alanine:D-serine ligase (ADP-forming)
Comments: The product of this enzyme, D-alanyl-D-serine, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide, which is formed by EC 6.3.2.4, D-alanine—D-alanine ligase. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dutka-Malen, S., Molinas, C., Arthur, M. and Courvalin, P. Sequence of the vanC gene of Enterococcus gallinarum BM4174 encoding a D-alanine:D-alanine ligase-related protein necessary for vancomycin resistance. Gene 112 (1992) 53–58. [DOI] [PMID: 1551598]
2.  Park, I.S., Lin, C.H. and Walsh, C.T. Bacterial resistance to vancomycin: overproduction, purification, and characterization of VanC2 from Enterococcus casseliflavus as a D-Ala-D-Ser ligase. Proc. Natl. Acad. Sci. USA 94 (1997) 10040–10044. [DOI] [PMID: 9294159]
3.  Fines, M., Perichon, B., Reynolds, P., Sahm, D.F. and Courvalin, P. VanE, a new type of acquired glycopeptide resistance in Enterococcus faecalis BM4405. Antimicrob. Agents Chemother. 43 (1999) 2161–2164. [PMID: 10471558]
4.  Depardieu, F., Bonora, M.G., Reynolds, P.E. and Courvalin, P. The vanG glycopeptide resistance operon from Enterococcus faecalis revisited. Mol. Microbiol. 50 (2003) 931–948. [DOI] [PMID: 14617152]
5.  Watanabe, S., Kobayashi, N., Quinones, D., Hayakawa, S., Nagashima, S., Uehara, N. and Watanabe, N. Genetic diversity of the low-level vancomycin resistance gene vanC-2/vanC-3 and identification of a novel vanC subtype (vanC-4) in Enterococcus casseliflavus. Microb. Drug Resist. 15 (2009) 1–9. [DOI] [PMID: 19216682]
[EC 6.3.2.35 created 2010]
 
 
EC 6.3.2.36     
Accepted name: 4-phosphopantoate—β-alanine ligase
Reaction: ATP + (R)-4-phosphopantoate + β-alanine = AMP + diphosphate + (R)-4′-phosphopantothenate
Other name(s): phosphopantothenate synthetase; TK1686 protein
Systematic name: (R)-4-phosphopantoate:β-alanine ligase (AMP-forming)
Comments: The conversion of (R)-pantoate to (R)-4′-phosphopantothenate is part of the pathway leading to biosynthesis of 4′-phosphopantetheine, an essential cofactor of coenzyme A and acyl-carrier protein. In bacteria and eukaryotes this conversion is performed by condensation with β-alanine, followed by phosphorylation (EC 6.3.2.1 [pantoate—β-alanine ligase] and EC 2.7.1.33 [pantothenate kinase], respectively). In archaea the order of these two steps is reversed, and phosphorylation precedes condensation with β-alanine. The two archaeal enzymes that catalyse this conversion are EC 2.7.1.169, pantoate kinase, and this enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Yokooji, Y., Tomita, H., Atomi, H. and Imanaka, T. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J. Biol. Chem. 284 (2009) 28137–28145. [DOI] [PMID: 19666462]
[EC 6.3.2.36 created 2011]
 
 
EC 6.3.2.37     
Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate + D-lysine = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-Nε-D-lysine
Glossary: muramic acid = 2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose
Other name(s): UDP-MurNAc-L-Ala-D-Glu:D-Lys ligase; D-lysine-adding enzyme
Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate:D-lysine γ-ligase (ADP-forming)
Comments: Involved in the synthesis of cell-wall peptidoglycan. The D-lysine is attached to the peptide chain at the N6 position. The enzyme from Thermotoga maritima also performs the reaction of EC 6.3.2.7, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Boniface, A., Bouhss, A., Mengin-Lecreulx, D. and Blanot, D. The MurE synthetase from Thermotoga maritima is endowed with an unusual D-lysine adding activity. J. Biol. Chem. 281 (2006) 15680–15686. [DOI] [PMID: 16595662]
[EC 6.3.2.37 created 2011, modified 2015]
 
 
EC 6.3.2.38     
Accepted name: N2-citryl-N6-acetyl-N6-hydroxylysine synthase
Reaction: 2 ATP + citrate + N6-acetyl-N6-hydroxy-L-lysine + H2O = 2 ADP + 2 phosphate + N6-acetyl-N2-citryl-N6-hydroxy-L-lysine
For diagram of aerobactin biosynthesis, click here
Glossary: citryl = 3-hydroxy-3,4-dicarboxybutanoyl
Other name(s): Nα-citryl-Nε-acetyl-Nε-hydroxylysine synthase; iucA (gene name)
Systematic name: citrate:N6-acetyl-N6-hydroxy-L-lysine ligase (AMP-forming)
Comments: Requires Mg2+. The enzyme is involved in the biosynthesis of aerobactin, a dihydroxamate siderophore. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme is believed to form an adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175–184. [DOI] [PMID: 4313071]
2.  Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N6-acetyl-N6-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096–3101.
3.  de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570–578. [DOI] [PMID: 2935523]
4.  Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437–443.
5.  Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601–611. [DOI] [PMID: 15719346]
6.  Oves-Costales, D., Kadi, N. and Challis, G.L. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem. Commun. (Camb.) (2009) 6530–6541. [PMID: 19865642]
[EC 6.3.2.38 created 2012, modified 2019]
 
 
EC 6.3.2.39     
Accepted name: aerobactin synthase
Reaction: ATP + N2-citryl-N6-acetyl-N6-hydroxy-L-lysine + N6-acetyl-N6-hydroxy-L-lysine = AMP + diphosphate + aerobactin
For diagram of aerobactin biosynthesis, click here
Other name(s): iucC (gene name)
Systematic name: N2-citryl-N6-acetyl-N6-hydroxy-L-lysine:N6-acetyl-N6-hydroxy-L-lysine ligase (AMP-forming)
Comments: Requires Mg2+. The enzyme is involved in the biosynthesis of aerobactin, a dihydroxamate siderophore. It belongs to a class of siderophore synthases known as type C nonribosomal peptide synthase-independent synthases (NIS). Type C enzymes are responsible for the formation of amide or ester bonds between a variety of substrates and a prochiral carboxyl group of a citrate molecule that is already linked to a different moiety at its other prochiral carboxyl group. The enzyme is believed to form an adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175–184. [DOI] [PMID: 4313071]
2.  Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N6-acetyl-N6-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096–3101.
3.  Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437–443.
4.  de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570–578. [DOI] [PMID: 2935523]
5.  de Lorenzo, V. and Neilands, J.B. Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli. J. Bacteriol. 167 (1986) 350–355. [DOI] [PMID: 3087960]
6.  Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601–611. [DOI] [PMID: 15719346]
7.  Oves-Costales, D., Kadi, N. and Challis, G.L. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem. Commun. (Camb.) (2009) 6530–6541. [PMID: 19865642]
[EC 6.3.2.39 created 2012, modified 2019]
 
 
EC 6.3.2.40     
Accepted name: cyclopeptine synthase
Reaction: 2 ATP + S-adenosyl-L-methionine + anthranilate + L-phenylalanine = cyclopeptine + 2 AMP + 2 diphosphate + S-adenosyl-L-homocysteine
For diagram of cyclopeptine, cyclopenine and viridicatin biosynthesis, click here
Glossary: cyclopeptine = (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
4′-methoxycyclopeptine = (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
Systematic name: S-adenosyl-L-methionine:anthranilate:L-phenylalanine ligase (cyclopeptine-forming)
Comments: Cyclopeptine synthase is the key enzyme of benzodiazepine alkaloid biosynthesis in several fungi species. The enzyme is a non-ribosomal peptide synthase. It is also active with O-methyl-L-tyrosine forming 4′-methoxycyclopeptine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lerbs, W. and Luckner, M. Cyclopeptine synthetase activity in surface cultures of Penicillium cyclopium. J. Basic Microbiol. 25 (1985) 387–391. [DOI] [PMID: 2995633]
2.  Gerlach, M, Schwelle, N., Lerbs, W. and Luckner, M. Enzymatic synthesis of cyclopeptine intermediates in Penicillium cyclopium. Phytochemistry 24 (1985) 1935–1939.
3.  Ishikawa, N., Tanaka, H., Koyama, F., Noguchi, H., Wang, C.C., Hotta, K. and Watanabe, K. Non-heme dioxygenase catalyzes atypical oxidations of 6,7-bicyclic systems to form the 6,6-quinolone core of viridicatin-type fungal alkaloids. Angew. Chem. Int. Ed. Engl. 53 (2014) 12880–12884. [DOI] [PMID: 25251934]
[EC 6.3.2.40 created 2013]
 
 
EC 6.3.2.41     
Accepted name: N-acetylaspartylglutamate synthase
Reaction: ATP + N-acetyl-L-aspartate + L-glutamate = ADP + phosphate + N-acetyl-L-aspartyl-L-glutamate
Other name(s): N-acetylaspartylglutamate synthetase; NAAG synthetase; NAAGS; RIMKLA (gene name) (ambiguous); RIMKLB (gene name) (ambiguous)
Systematic name: N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamate-forming)
Comments: The enzyme, found in animals, produces the neurotransmitter N-acetyl-L-aspartyl-L-glutamate. One isoform also has the activity of EC 6.3.1.17, β-citrylglutamate synthase [2], while another isoform has the activity of EC 6.3.2.42, N-acetylaspartylglutamylglutamate synthase [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Becker, I., Lodder, J., Gieselmann, V. and Eckhardt, M. Molecular characterization of N-acetylaspartylglutamate synthetase. J. Biol. Chem. 285 (2010) 29156–29164. [DOI] [PMID: 20643647]
2.  Collard, F., Stroobant, V., Lamosa, P., Kapanda, C.N., Lambert, D.M., Muccioli, G.G., Poupaert, J.H., Opperdoes, F. and Van Schaftingen, E. Molecular identification of N-acetylaspartylglutamate synthase and β-citrylglutamate synthase. J. Biol. Chem. 285 (2010) 29826–29833. [DOI] [PMID: 20657015]
3.  Lodder-Gadaczek, J., Becker, I., Gieselmann, V., Wang-Eckhardt, L. and Eckhardt, M. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. J. Biol. Chem. 286 (2011) 16693–16706. [DOI] [PMID: 21454531]
[EC 6.3.2.41 created 2014]
 
 
EC 6.3.2.42     
Accepted name: N-acetylaspartylglutamylglutamate synthase
Reaction: 2 ATP + N-acetyl-L-aspartate + 2 L-glutamate = 2 ADP + 2 phosphate + N-acetyl-L-aspartyl-L-glutamyl-L-glutamate
Other name(s): N-acetylaspartylglutamylglutamate synthetase; NAAG(2) synthase; NAAG synthetase II; NAAGS-II; RIMKLA (gene name) (ambiguous)
Systematic name: N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamyl-L-glutamate-forming)
Comments: The enzyme, found in mammals, also has the activity of EC 6.3.2.41, N-acetylaspartylglutamate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lodder-Gadaczek, J., Becker, I., Gieselmann, V., Wang-Eckhardt, L. and Eckhardt, M. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. J. Biol. Chem. 286 (2011) 16693–16706. [DOI] [PMID: 21454531]
[EC 6.3.2.42 created 2014]
 
 
EC 6.3.2.43     
Accepted name: [amino-group carrier protein]—L-2-aminoadipate ligase
Reaction: ATP + an [amino-group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + an [amino-group carrier protein]-C-terminal-[N-(1,4-dicarboxybutyl)-L-glutamine]
Other name(s): α-aminoadipate-lysW ligase; lysX (gene name); LysX (ambiguous); AAA—LysW ligase; [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate:L-2-aminoadipate ligase (ADP-forming); [lysine-biosynthesis-protein LysW]—L-2-aminoadipate ligase
Systematic name: [amino-group carrier protein]-C-terminal-L-glutamate:L-2-aminoadipate ligase (ADP-forming)
Comments: The enzymes from the thermophilic bacterium Thermus thermophilus and the thermophilic archaea Sulfolobus acidocaldarius and Sulfolobus tokodaii protect the amino group of L-2-aminoadipate by conjugation to the carrier protein LysW. This reaction is part of the lysine biosynthesis pathway in these organisms.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Vassylyeva, M.N., Sakai, H., Matsuura, T., Sekine, S., Nishiyama, M., Terada, T., Shirouzu, M., Kuramitsu, S., Vassylyev, D.G. and Yokoyama, S. Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 1651–1652. [PMID: 12925802]
2.  Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]
3.  Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277–283. [DOI] [PMID: 23434852]
[EC 6.3.2.43 created 2014, modified 2019]
 
 
EC 6.3.2.44     
Accepted name: pantoate—β-alanine ligase (ADP-forming)
Reaction: ATP + (R)-pantoate + β-alanine = ADP + phosphate + (R)-pantothenate
For diagram of coenzyme A biosynthesis (early stages), click here
Glossary: (R)-pantoate = (2R)-2,4-dihydroxy-3,3-dimethylbutanoate
(R)-pantothenate = 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoate
Other name(s): pantothenate synthetase (ambiguous); pantoate—β-alanine ligase (ambiguous)
Systematic name: (R)-pantoate:β-alanine ligase (ADP-forming)
Comments: The enzyme, characterized from the archaeon Methanosarcina mazei, is involved in the biosynthesis of pantothenate. It is different from EC 6.3.2.1, the AMP-forming pantoate-β-alanine ligase found in bacteria and eukaryota.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ronconi, S., Jonczyk, R. and Genschel, U. A novel isoform of pantothenate synthetase in the Archaea. FEBS J. 275 (2008) 2754–2764. [DOI] [PMID: 18422645]
[EC 6.3.2.44 created 2014]
 
 
EC 6.3.2.45     
Accepted name: UDP-N-acetylmuramate—L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioate ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramate + L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioate
Glossary: meso-2,6-diaminoheptanedioate = meso-2,6-diaminopimelate
Other name(s): murein peptide ligase; Mpl; yjfG (gene name); UDP-MurNAc:L-Ala-γ-D-Glu-meso-A2pm ligase; UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminopimelate ligase
Systematic name: UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioate ligase2015
Comments: The enzyme catalyses the reincorporation into peptidoglycan of the tripeptide L-alanyl-γ-D-glutamyl-2,6-meso-diaminoheptanedioate released during the maturation and constant remodeling of this bacterial cell wall polymer that occur during cell growth and division. The enzyme can also use the tetrapeptide L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioyl-D-alanine or the pentapeptide L-alanyl-γ-D-glutamyl-meso-2,6-diaminoheptanedioyl-D-alanyl-D-alanine in vivo and in vitro. Requires Mg2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Mengin-Lecreulx, D., van Heijenoort, J. and Park, J.T. Identification of the mpl gene encoding UDP-N-acetylmuramate: L-alanyl-γ-D-glutamyl-meso-diaminopimelate ligase in Escherichia coli and its role in recycling of cell wall peptidoglycan. J. Bacteriol. 178 (1996) 5347–5352. [DOI] [PMID: 8808921]
2.  Herve, M., Boniface, A., Gobec, S., Blanot, D. and Mengin-Lecreulx, D. Biochemical characterization and physiological properties of Escherichia coli UDP-N-acetylmuramate:L-alanyl-γ-D-glutamyl-meso-diaminopimelate ligase. J. Bacteriol. 189 (2007) 3987–3995. [DOI] [PMID: 17384195]
[EC 6.3.2.45 created 2014]
 
 
EC 6.3.2.46     
Accepted name: fumarate—(S)-2,3-diaminopropanoate ligase
Reaction: ATP + fumarate + L-2,3-diaminopropanoate = AMP + diphosphate + N3-fumaroyl-L-2,3-diaminopropanoate
Glossary: N3-fumaroyl-L-2,3-diaminopropanoate = (2E)-4-{[(2S)-2-amino-2-carboxyethyl]amino}-4-oxobut-2-enoate
L-2,3-diaminopropanoate = (S)-2,3-diaminopropanoate
Other name(s): DdaG; fumarate:(S)-2,3-diaminopropanoate ligase (AMP-forming)
Systematic name: fumarate:L-2,3-diaminopropanoate ligase (AMP-forming)
Comments: The enzyme, characterized from the bacterium Enterobacter agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an L-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hollenhorst, M.A., Clardy, J. and Walsh, C.T. The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics. Biochemistry 48 (2009) 10467–10472. [DOI] [PMID: 19807062]
[EC 6.3.2.46 created 2015]
 
 
EC 6.3.2.47     
Accepted name: dapdiamide synthase
Reaction: (1) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-valine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
(2) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-isoleucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
(3) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-leucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine
(4) ATP + 3-({[(2R,3R)-3-carbamoyloxiran-2-yl]carbonyl}amino)-L-alanine + L-valine = ADP + phosphate + 3-({[(2R,3R)-3-carbamoyloxiran-2-yl]carbonyl}amino)-L-alanyl-L-valine
Glossary: dapdiamide A = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
dapdiamide B = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
dapdiamide C = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine
Other name(s): DdaF; dapdiamide A synthase
Systematic name: 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine:L-valine ligase (ADP-forming)
Comments: The enzyme, characterized from the bacterium Pantoea agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an (S)-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hollenhorst, M.A., Clardy, J. and Walsh, C.T. The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics. Biochemistry 48 (2009) 10467–10472. [DOI] [PMID: 19807062]
2.  Hollenhorst, M.A., Bumpus, S.B., Matthews, M.L., Bollinger, J.M., Jr., Kelleher, N.L. and Walsh, C.T. The nonribosomal peptide synthetase enzyme DdaD tethers N(β)-fumaramoyl-L-2,3-diaminopropionate for Fe(II)/α-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis. J. Am. Chem. Soc. 132 (2010) 15773–15781. [DOI] [PMID: 20945916]
[EC 6.3.2.47 created 2015, modified 2016]
 
 
EC 6.3.2.48     
Accepted name: L-arginine-specific L-amino acid ligase
Reaction: ATP + L-arginine + an L-amino acid = ADP + phosphate + an L-arginyl-L-amino acid
Other name(s): RizA; L-amino acid ligase RizA
Systematic name: L-arginine:L-amino acid ligase (ADP-forming)
Comments: The enzyme, characterized from the bacterium Bacillus subtilis, requires Mn2+ for activity. It shows strict substrate specificity toward L-arginine as the first (N-terminal) amino acid of the product. The second amino acid could be any standard protein-building amino acid except for L-proline.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kino, K., Kotanaka, Y., Arai, T. and Yagasaki, M. A novel L-amino acid ligase from Bacillus subtilis NBRC3134, a microorganism producing peptide-antibiotic rhizocticin. Biosci. Biotechnol. Biochem. 73 (2009) 901–907. [DOI] [PMID: 19352016]
[EC 6.3.2.48 created 2015]
 
 
EC 6.3.2.49     
Accepted name: L-alanine—L-anticapsin ligase
Reaction: ATP + L-alanine + L-anticapsin = ADP + phosphate + bacilysin
For diagram of bacilysin biosynthesis, click here
Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
bacilysin = L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
Other name(s): BacD; alanine-anticapsin ligase; L-Ala-L-anticapsin ligase; ywfE (gene name)
Systematic name: L-alanine:L-anticapsin ligase (ADP-forming)
Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. The enzyme requires Mg2+ or Mn2+ for activity, and has a broad substrate specificity in vitro [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Tabata, K., Ikeda, H. and Hashimoto, S. ywfE in Bacillus subtilis codes for a novel enzyme, L-amino acid ligase. J. Bacteriol. 187 (2005) 5195–5202. [DOI] [PMID: 16030213]
2.  Tsuda, T., Suzuki, T. and Kojima, S. Crystallization and preliminary X-ray diffraction analysis of Bacillus subtilis YwfE, an L-amino-acid ligase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 203–206. [DOI] [PMID: 22298000]
3.  Shomura, Y., Hinokuchi, E., Ikeda, H., Senoo, A., Takahashi, Y., Saito, J., Komori, H., Shibata, N., Yonetani, Y. and Higuchi, Y. Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis. Protein Sci. 21 (2012) 707–716. [DOI] [PMID: 22407814]
4.  Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889–901. [DOI] [PMID: 23317005]
[EC 6.3.2.49 created 2006 as EC 6.3.2.28, transferred 2015 to EC 6.3.2.49]
 
 
EC 6.3.2.50     
Accepted name: tenuazonic acid synthetase
Reaction: ATP + L-isoleucine + acetoacetyl-CoA = AMP + diphosphate + tenuazonic acid + CoA
Glossary: tenuazonic acid = (5S)-3-acetyl-5-[(2S)-butan-2-yl]-4-hydroxy-1,5-dihydro-2H-pyrrol-2-one
Other name(s): TAS1 (gene name)
Systematic name: L-isoleucine:acetoacetyl-CoA ligase (tenuazonic acid-forming)
Comments: This fungal enzyme, isolated from Magnaporthe oryzae, is an non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) hybrid protein that consists of condensation (C), adenylation (A) and peptidyl-carrier protein (PCP) domains in the NRPS portion and a ketosynthase (KS) domain in the PKS portion. ATP is required for activation of isoleucine, which is then condensed with acetoacetyl-CoA. Cyclization and release from the enzyme are catalysed by the KS domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Yun, C.S., Motoyama, T. and Osada, H. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme. Nat. Commun. 6:8758 (2015). [DOI] [PMID: 26503170]
[EC 6.3.2.50 created 2017]
 
 
EC 6.3.2.51     
Accepted name: phosphopantothenate—cysteine ligase (ATP)
Reaction: ATP + (R)-4′-phosphopantothenate + L-cysteine = AMP + diphosphate + N-[(R)-4′-phosphopantothenoyl]-L-cysteine
For diagram of the late stages of CoA biosynthesis, click here
Other name(s): phosphopantothenoylcysteine synthetase (ambiguous); PPCS (gene name)
Systematic name: (R)-4′-phosphopantothenate:L-cysteine ligase (ATP-utilizing)
Comments: A key enzyme in the production of coenzyme A. The eukaryotic enzyme requires ATP, in contrast to the bacterial enzyme, EC 6.3.2.5, phosphopantothenate—cysteine ligase, which requires CTP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-50-1
References:
1.  Daugherty, M. Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem. 277 (2002) 21431–21439. [DOI] [PMID: 11923312]
2.  Manoj, N., Strauss, E., Begley, T.P. and Ealick, S.E. Structure of human phosphopantothenoylcysteine synthetase at 2.3 Å Resolution. Structure 11 (2003) 927–936. [DOI] [PMID: 12906824]
3.  Kupke, T., Hernandez-Acosta, P. and Culianez-Macia, F.A. 4′-phosphopantetheine and coenzyme A biosynthesis in plants. J. Biol. Chem. 278 (2003) 38229–38237. [DOI] [PMID: 12860978]
[EC 6.3.2.51 created 2017]
 
 
EC 6.3.2.52     
Accepted name: jasmonoyl—L-amino acid ligase
Reaction: ATP + jasmonate + an L-amino acid = AMP + diphosphate + a jasmonoyl-L-amino acid
Other name(s): JAR1 (gene name); JAR4 (gene name); JAR6 (gene name); jasmonoyl—L-amino acid synthetase
Systematic name: jasmonate:L-amino acid ligase
Comments: Two jasmonoyl-L-amino acid synthetases have been described from Nicotiana attenuata [3] and one from Arabidopsis thaliana [1]. The N. attenuata enzymes generate jasmonoyl-L-isoleucine, jasmonoyl-L-leucine, and jasmonoyl-L-valine. The enzyme from A. thaliana could catalyse the addition of many different amino acids to jasmonate in vitro [1,4,5]. While the abundant form of jasmonate in plants is (–)-jasmonate, the active form of jasmonoyl-L-isoleucine is (+)-7-iso-jasmonoyl-L-isoleucine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Staswick, P.E. and Tiryaki, I. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell 16 (2004) 2117–2127. [DOI] [PMID: 15258265]
2.  Kang, J.H., Wang, L., Giri, A. and Baldwin, I.T. Silencing threonine deaminase and JAR4 in Nicotiana attenuata impairs jasmonic acid-isoleucine-mediated defenses against Manduca sexta. Plant Cell 18 (2006) 3303–3320. [DOI] [PMID: 17085687]
3.  Wang, L., Halitschke, R., Kang, J.H., Berg, A., Harnisch, F. and Baldwin, I.T. Independently silencing two JAR family members impairs levels of trypsin proteinase inhibitors but not nicotine. Planta 226 (2007) 159–167. [DOI] [PMID: 17273867]
4.  Guranowski, A., Miersch, O., Staswick, P.E., Suza, W. and Wasternack, C. Substrate specificity and products of side-reactions catalyzed by jasmonate:amino acid synthetase (JAR1). FEBS Lett. 581 (2007) 815–820. [DOI] [PMID: 17291501]
5.  Suza, W.P. and Staswick, P.E. The role of JAR1 in jasmonoyl-L-isoleucine production during Arabidopsis wound response. Planta 227 (2008) 1221–1232. [DOI] [PMID: 18247047]
[EC 6.3.2.52 created 2018, modified 2019]
 
 
EC 6.3.2.53     
Accepted name: UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase
Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanine + L-glutamate = ADP + phosphate + UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate
Other name(s): murD2 (gene name); UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate synthetase; UDP-MurNAc-L-Ala-L-Glu synthetase
Systematic name: UDP-N-acetylmuramoyl-L-alanine—L-glutamate ligase (ADP-forming)
Comments: The enzyme, characterized from the bacterium Xanthomonas oryzae, catalyses the ligation of a terminal L-glutamate to UDP-N-acetyl-α-D-muramoyl-L-alanine. The combined activity of this enzyme and EC 5.1.1.23, UDP-N-acetyl-α-D-muramoyl-L-alanyl-L-glutamate epimerase, provides an alternative route for incorporating D-glutamate into peptidoglycan, replacing the more common combination of EC 5.1.1.3, glutamate racemase, and EC 6.3.2.9, UDP-N-acetylmuramoyl-L-alanine—D-glutamate ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Feng, R., Satoh, Y., Ogasawara, Y., Yoshimura, T. and Dairi, T. A glycopeptidyl-glutamate epimerase for bacterial peptidoglycan biosynthesis. J. Am. Chem. Soc. 139 (2017) 4243–4245. [PMID: 28294606]
[EC 6.3.2.53 created 2018]
 
 
EC 6.3.2.54     
Accepted name: L-2,3-diaminopropanoate—citrate ligase
Reaction: ATP + L-2,3-diaminopropanoate + citrate = AMP + diphosphate + 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate
Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate
Other name(s): sbnE (gene name); 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate synthtase
Systematic name: L-2,3-diaminopropanoate:citrate ligase (2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate-forming)
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A NIS enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme forms a citrate adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dale, S.E., Doherty-Kirby, A., Lajoie, G. and Heinrichs, D.E. Role of siderophore biosynthesis in virulence of Staphylococcus aureus: identification and characterization of genes involved in production of a siderophore. Infect. Immun. 72 (2004) 29–37. [PMID: 14688077]
2.  Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594–608. [PMID: 19775248]
[EC 6.3.2.54 created 2019]
 
 
EC 6.3.2.55     
Accepted name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate synthase
Reaction: ATP + 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate + L-2,3-diaminopropanoate = AMP + diphosphate + 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate
Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate
Other name(s): sbnF (gene name)
Systematic name: 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate:L-2,3-diaminopropanoate ligase {2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate-forming}
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type C nonribosomal peptide synthase-independent synthases (NIS). Type C NIS enzymes recognize esterified or amidated derivatives of carboxylic acids. The enzyme likely forms a 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594–608. [PMID: 19775248]
[EC 6.3.2.55 created 2019]
 
 
EC 6.3.2.56     
Accepted name: staphyloferrin B synthase
Reaction: ATP + 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate + 2-oxoglutarate = AMP + diphosphate + staphyloferrin B
Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate
Other name(s): sbnC (gene name)
Systematic name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate:2-oxoglutarate ligase (staphyloferrin B-forming)
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, catalyses the last step in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type B nonribosomal peptide synthase-independent synthases (NIS). Type B NIS enzymes recognize the δ-acid group of 2-oxoglutarate. The enzyme forms a 2-oxoglutarate adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594–608. [PMID: 19775248]
[EC 6.3.2.56 created 2019]
 
 
EC 6.3.2.57     
Accepted name: staphyloferrin A synthase
Reaction: ATP + N5-[(S)-citryl]-D-ornithine + citrate = AMP + diphosphate + staphyloferrin A
For diagram of staphyloferrin A biosynthesis, click here
Glossary: staphyloferrin A = N2-[(R)-citryl],N5-[(S)-citryl]-D-ornithine
citryl = 3-hydroxy-3,4-dicarboxybutanoyl
Other name(s): sfnaB (gene name)
Systematic name: N5-[(S)-citryl]-D-ornithine:citrate ligase (staphyloferrin A-forming)
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, catalyses the last step in the biosynthesis of the siderophore staphyloferrin A. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A NIS enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme forms a citrate adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cotton, J.L., Tao, J. and Balibar, C.J. Identification and characterization of the Staphylococcus aureus gene cluster coding for staphyloferrin A. Biochemistry 48 (2009) 1025–1035. [PMID: 19138128]
[EC 6.3.2.57 created 2019]
 
 
EC 6.3.2.58     
Accepted name: D-ornithine—citrate ligase
Reaction: ATP + D-ornithine + citrate = AMP + diphosphate + N5-[(S)-citryl]-D-ornithine
For diagram of staphyloferrin A biosynthesis, click here
Glossary: staphyloferrin A = N2-[(R)-citryl],N5-[(S)-citryl]-D-ornithine
Other name(s): sfnaD (gene name)
Systematic name: D-ornithine:citrate ligase {3-[(2-aminopentan-5-oylcarbamoyl)methyl]-3-hydroxybutanoate-forming}
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin A. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A NIS enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme forms a citrate adenylate intermediate prior to ligation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cotton, J.L., Tao, J. and Balibar, C.J. Identification and characterization of the Staphylococcus aureus gene cluster coding for staphyloferrin A. Biochemistry 48 (2009) 1025–1035. [PMID: 19138128]
[EC 6.3.2.58 created 2019]
 
 
EC 6.3.2.59     
Accepted name: 3-methyl-D-ornithine—L-lysine ligase
Reaction: ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine
Glossary: L-pyrrolysine = N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
Other name(s): N6-[(2R,3R)-3-methylornithyl]-L-lysine synthase; 3-methylornithine—L-lysine ligase; pylC (gene name)
Systematic name: (3R)-3-methyl-D-ornithine:L-lysine γ-ligase (ADP-forming)
Comments: The enzyme participates in the biosynthesis of L-pyrrolysine, a naturally occurring, genetically coded amino acid found in some methanogenic archaea and a few bacterial species. L-pyrrolysine is present in several methyltransferases that are involved in methyl transfer from methylated amine compounds to coenzyme M.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Gaston, M.A., Zhang, L., Green-Church, K.B. and Krzycki, J.A. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471 (2011) 647–650. [DOI] [PMID: 21455182]
2.  Cellitti, S.E., Ou, W., Chiu, H.P., Grunewald, J., Jones, D.H., Hao, X., Fan, Q., Quinn, L.L., Ng, K., Anfora, A.T., Lesley, S.A., Uno, T., Brock, A. and Geierstanger, B.H. D-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine. Nat. Chem. Biol. 7 (2011) 528–530. [DOI] [PMID: 21525873]
3.  Quitterer, F., List, A., Beck, P., Bacher, A. and Groll, M. Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution. J. Mol. Biol. 424 (2012) 270–282. [DOI] [PMID: 22985965]
[EC 6.3.2.59 created 2021]
 
 
EC 6.3.2.60     
Accepted name: glutamate—[amino group carrier protein] ligase
Reaction: ATP + L-glutamate + an [amino-group carrier protein]-C-terminal-L-glutamate = ADP + phosphate + an [amino-group carrier protein]-C-terminal-γ-(L-glutamyl)-L-glutamate
Other name(s): argX (gene name)
Systematic name: L-glutamate:an [amino-group carrier protein]-C-terminal-L-glutamate ligase (ADP-forming)
Comments: The enzyme, originally characterized from the archaeon Sulfolobus acidocaldarius, is involved in L-arginine biosynthesis. The enzyme from the archaeon Thermococcus kodakarensis is bifunctional and also catalyses the activity of EC 6.3.2.43, [amino-group carrier protein]—L-2-aminoadipate ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277–283. [DOI] [PMID: 23434852]
2.  Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630–21643. [DOI] [PMID: 27566549]
[EC 6.3.2.60 created 2021]
 
 
EC 6.3.2.61     
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Regnard, C., Audebert, S., Desbruyeres, Denoulet, P. and Edde, B. Tubulin polyglutamylase: partial purification and enzymatic properties. Biochemistry 37 (1998) 8395–8404. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 18045879]
[EC 6.3.2.61 created 2021]
 
 
EC 6.3.2.62     
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Regnard, C., Audebert, S., Desbruyeres, Denoulet, P. and Edde, B. Tubulin polyglutamylase: partial purification and enzymatic properties. Biochemistry 37 (1998) 8395–8404. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 18045879]
[EC 6.3.2.62 created 2021]
 
 
EC 6.3.2.63     
Accepted name: putrebactin synthase
Reaction: 2 ATP + 2 N1-hydroxy-N1-succinylputrescine = 2 AMP + 2 diphosphate + putrebactin (overall reaction)
(1a) ATP + 2 N1-hydroxy-N1-succinylputrescine = AMP + diphosphate + pre-putrebactin
(1b) ATP + pre-putrebactin = AMP + diphosphate + putrebactin
Glossary: putrebactin = 1,11-dihydroxy-1,6,11,16-tetraazacycloicosane-2,5,12,15-tetrone
pre-putrebactin = 4-{[4-({4-[(4-aminobutyl)(hydroxy)amino]-4-oxobutanoyl}amino)butyl](hydroxy)amino}-4-oxobutanoate
Other name(s): pubC (gene name)
Systematic name: N1-hydroxy-N1-succinylputrescine:N1-hydroxy-N1-succinylputrescine ligase
Comments: Requires Mg2+. The enzyme, characterized from the bacteria Shewanella spp. MR-4 and MR-7, catalyse the last step in the biosynthesis of the siderophore putrebactin. The enzyme catalyses the reaction in two steps - concatenation of two molecules of N1-hydroxy-N1-succinylputrescine, followed by cyclization.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kadi, N., Arbache, S., Song, L., Oves-Costales, D. and Challis, G.L. Identification of a gene cluster that directs putrebactin biosynthesis in Shewanella species: PubC catalyzes cyclodimerization of N-hydroxy-N-succinylputrescine. J. Am. Chem. Soc. 130 (2008) 10458–10459. [DOI] [PMID: 18630910]
[EC 6.3.2.63 created 2024]
 
 
EC 6.3.2.64     
Accepted name: bisucaberin synthase
Reaction: 2 ATP + 2 N1-hydroxy-N1-succinylcadaverine = 2 AMP + 2 diphosphate + bisucaberin (overall reaction)
(1a) ATP + 2 N1-hydroxy-N1-succinylcadaverine = AMP + diphosphate + bisucaberin B
(1b) ATP + bisucaberin B = AMP + diphosphate + bisucaberin
Glossary: bisucaberin B = pre-bisucaberin = 3-[(5-{3-[(5-aminopentyl)(hydroxy)carbamoyl]propanamido}pentyl)(hydroxy)carbamoyl]propanoate
bisucaberin = 1,12-dihydroxy-1,6,12,17-tetrazacyclodocosane-2,5,13,16-tetrone
Other name(s): pubC (gene name); BibC C-terminal domain
Systematic name: N1-hydroxy-N1-succinylcadaverine:N1-hydroxy-N1-succinylcadaverine ligase
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Aliivibrio salmonicida, catalyses the last step in the biosynthesis of the siderophore bisucaberin. The enzyme catalyses the reaction in two steps - concatenation of two molecules of N1-hydroxy-N1-succinylcadaverine, followed by cyclization.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kadi, N., Song, L. and Challis, G.L. Bisucaberin biosynthesis: an adenylating domain of the BibC multi-enzyme catalyzes cyclodimerization of N-hydroxy-N-succinylcadaverine. Chem. Commun. (Camb.) (2008) 5119–5121. [DOI] [PMID: 18956041]
[EC 6.3.2.64 created 2024]
 
 
EC 6.3.3.1     
Accepted name: phosphoribosylformylglycinamidine cyclo-ligase
Reaction: ATP + 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
For diagram of the early stages of purine biosynthesis, click here
Other name(s): phosphoribosylaminoimidazole synthetase; AIR synthetase; 5′-aminoimidazole ribonucleotide synthetase; 2-(formamido)-1-N-(5-phosphoribosyl)acetamidine cyclo-ligase (ADP-forming)
Systematic name: 2-(formamido)-N1-(5-phosphoribosyl)acetamidine cyclo-ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-53-4
References:
1.  Levenberg, B. and Buchanan, J.M. Properties of the purines. XII. Structure, enzymatic synthesis, and metabolism of 5-aminoimidazole ribotide. J. Biol. Chem. 224 (1957) 1005–1018. [PMID: 13405929]
2.  Levenberg, B. and Buchanan, J.M. Biosynthesis of the purines. XIII. Structure, enzymatic synthesis, and metabolism of (α-N-formyl)-glycinamidine ribotide. J. Biol. Chem. 224 (1957) 1018–1027. [PMID: 13405930]
[EC 6.3.3.1 created 1961, modified 2000]
 
 
EC 6.3.3.2     
Accepted name: 5-formyltetrahydrofolate cyclo-ligase
Reaction: ATP + 5-formyltetrahydrofolate = ADP + phosphate + 5,10-methenyltetrahydrofolate
For diagram of folate cofactors, click here and for diagram of C1 metabolism, click here
Other name(s): 5,10-methenyltetrahydrofolate synthetase; formyltetrahydrofolic cyclodehydrase; 5-formyltetrahydrofolate cyclodehydrase
Systematic name: 5-formyltetrahydrofolate cyclo-ligase (ADP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37318-64-2
References:
1.  Greenberg, D.M., Wynston, L.K. and Nagabhushanan, A. Further studies on N5-formyltetrahydrofolic acid cyclodehydrase. Biochemistry 4 (1965) 1872–1878.
[EC 6.3.3.2 created 1972]
 
 
EC 6.3.3.3     
Accepted name: dethiobiotin synthase
Reaction: ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
Other name(s): desthiobiotin synthase
Systematic name: 7,8-diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)
Comments: CTP has half the activity of ATP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-75-9
References:
1.  Krell, K. and Eisenberg, M.A. The purification and properties of dethiobiotin synthetase. J. Biol. Chem. 245 (1970) 6558–6566. [PMID: 4921568]
2.  Yang, H.-C., Tani, Y. and Ogata, K. Synthesis of biotin vitamers from biotin diaminocarboxylic acid or 7,8-diaminopelargonic acid by a purified enzyme of Pseudomonas graveolens. Agric. Biol. Chem. 34 (1970) 1748–1750.
[EC 6.3.3.3 created 1976]
 
 
EC 6.3.3.4     
Accepted name: (carboxyethyl)arginine β-lactam-synthase
Reaction: ATP + L-N2-(2-carboxyethyl)arginine = AMP + diphosphate + deoxyamidinoproclavaminate
For diagram of clavulanate biosynthesis, click here
Other name(s): L-2-N-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming)
Systematic name: L-N2-(2-carboxyethyl)arginine cyclo-ligase (AMP-forming)
Comments: Forms part of the pathway for the biosythesis of the β-lactamase inhibitor clavulanate in Streptomyces clavuligerus. It has been proposed [3] that L-N2-(2-carboxyethyl)arginine is first converted into an acyl-AMP by reaction with ATP and loss of diphosphate, and that the β-lactam ring is then formed by the intramolecular attack of the β-nitrogen on the activated carboxy group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhou, J., Kelly, W.L., Bachmann, B.O., Gunsior, M., Townsend, C.A. and Solomon, E.I. Spectroscopic studies of substrate interactions with clavaminate synthase 2, a multifunctional α-KG-dependent non-heme iron enzyme: Correlation with mechanisms and reactivities. J. Am. Chem. Soc. 123 (2001) 7388–7398. [DOI] [PMID: 11472170]
2.  Townsend, C.A. New reactions in clavulanic acid biosynthesis. Curr. Opin. Chem. Biol. 6 (2002) 583–589. [DOI] [PMID: 12413541]
3.  Bachmann, B.O., Li, R. and Townsend, C.A. β-Lactam synthetase: a new biosynthetic enzyme. Proc. Natl. Acad. Sci. USA 95 (1998) 9082–9086. [DOI] [PMID: 9689037]
[EC 6.3.3.4 created 2003]
 
 
EC 6.3.3.5     
Accepted name: O-ureido-D-serine cyclo-ligase
Reaction: O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + NH3 + ADP + phosphate
Glossary: O-ureido-D-serine = (2R)-2-amino-3-[(carbamoylamino)oxy]propanoate
Other name(s): dcsG (gene name)
Systematic name: O-ureido-D-serine cyclo-ligase (D-cycloserine-forming)
Comments: The enzyme participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132–1139. [DOI] [PMID: 20086163]
2.  Uda, N., Matoba, Y., Kumagai, T., Oda, K., Noda, M. and Sugiyama, M. Establishment of an in vitro D-cycloserine-synthesizing system by using O-ureido-L-serine synthase and D-cycloserine synthetase found in the biosynthetic pathway. Antimicrob. Agents Chemother. 57 (2013) 2603–2612. [DOI] [PMID: 23529730]
[EC 6.3.3.5 created 2013]
 
 


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