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Literature summary extracted from
- Peptide epimerization machineries found in microorganisms (2018), Front. Microbiol., 9, 156 .
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 5.1.1.20 | gene ycjG | Escherichia coli |
| 5.1.1.20 | gene yfkA or yfkB | Bacillus subtilis |
| 5.1.1.23 | gene murL, shotgun cloning experiment with DGlu auxotrophic Escherichia coli strain WM335 | Xanthomonas oryzae |
| 6.3.2.53 | expressed in Escherichia coli WM335 cells | Xanthomonas oryzae |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 5.1.1.20 | crystal structure of YcjG in apoform | Escherichia coli |
| 5.1.1.20 | crystal structure of YkfB in apoform and in complex with L-Ala-D/L-Glu | Bacillus subtilis |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.1.23 | Mg2+ | required | Xanthomonas oryzae |  |
| 6.3.2.53 | Mg2+ | required | Xanthomonas oryzae | |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.20 | L-alanyl-D-glutamate | Escherichia coli | - |
L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | L-alanyl-D-glutamate | Bacillus subtilis | - |
L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | L-alanyl-D-glutamate | Bacillus subtilis 168 | - |
L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | additional information | Escherichia coli | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | ? | - |
? | |
| 5.1.1.20 | additional information | Bacillus subtilis | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | ? | - |
? | |
| 5.1.1.20 | additional information | Bacillus subtilis 168 | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | ? | - |
? | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | Xanthomonas oryzae | - |
AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | Xanthomonas oryzae MAFF311018 | - |
AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 6.3.2.53 | ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + L-glutamate | Xanthomonas oryzae | - |
ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate | - |
? | |
| 6.3.2.53 | ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + L-glutamate | Xanthomonas oryzae MAFF311018 | - |
ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 5.1.1.20 | Bacillus subtilis | O34400 | - |
- |
| 5.1.1.20 | Bacillus subtilis 168 | O34400 | - |
- |
| 5.1.1.20 | Escherichia coli | P51981 | - |
- |
| 5.1.1.23 | Xanthomonas oryzae | Q5H398 | - |
- |
| 5.1.1.23 | Xanthomonas oryzae MAFF311018 | Q5H398 | - |
- |
| 6.3.2.53 | Xanthomonas oryzae | - |
- |
- |
| 6.3.2.53 | Xanthomonas oryzae MAFF311018 | - |
- |
- |
Reaction
| EC Number | Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|---|
| 5.1.1.20 | L-alanyl-D-glutamate = L-alanyl-L-glutamate | a two-base reaction mechanism typical for enolase superfamily enzymes, Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate, overview | Escherichia coli | |
| 5.1.1.20 | L-alanyl-D-glutamate = L-alanyl-L-glutamate | a two-base reaction mechanism typical for enolase superfamily enzymes, Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate, overview | Bacillus subtilis |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 5.1.1.20 | L-alanyl-D-glutamate | - |
Escherichia coli | L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | L-alanyl-D-glutamate | - |
Bacillus subtilis | L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | L-alanyl-D-glutamate | - |
Bacillus subtilis 168 | L-alanyl-L-glutamate | - |
? | |
| 5.1.1.20 | additional information | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | Escherichia coli | ? | - |
? | |
| 5.1.1.20 | additional information | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | Bacillus subtilis | ? | - |
? | |
| 5.1.1.20 | additional information | epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YcjG shows a broad substrate specificity against dipeptides with L-Ala at the N-terminus but narrow specificity against dipeptides with L-Glu at the C-terminus | Escherichia coli | ? | - |
? | |
| 5.1.1.20 | additional information | epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YkfB has a narrow substrate specificity against both N- and C-terminal substrates | Bacillus subtilis | ? | - |
? | |
| 5.1.1.20 | additional information | The kinetic parameters suggest that L-Ala-D/L-Glu is the intrinsic substrate for the enzyme | Bacillus subtilis 168 | ? | - |
? | |
| 5.1.1.20 | additional information | epimerization of the L-Glu residue is confirmed by NMR and MS analysis. Analyzing substrate specificity with dipeptides composed of different amino acids, YkfB has a narrow substrate specificity against both N- and C-terminal substrates | Bacillus subtilis 168 | ? | - |
? | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | - |
Xanthomonas oryzae | AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | the terminal L-Glu of the substrate is converted into D-Glu | Xanthomonas oryzae | AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | - |
Xanthomonas oryzae MAFF311018 | AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 5.1.1.23 | ATP + UDP-MurNAc-L-Ala-L-Glu | the terminal L-Glu of the substrate is converted into D-Glu | Xanthomonas oryzae MAFF311018 | AMP + diphosphate + UDP-MurNAc-L-Ala-D-Glu | - |
ir | |
| 5.1.1.23 | additional information | XOO_1319 is a distinct type of glycopeptidyl-glutamate epimerase and is designated XOO_1319 as UDP-MurNAc-LAla-L-Glu epimerase, MurL. It shows no activity in the reverse reaction with UDP-MurNAc-L-Ala-D-Glu. MurL requires ATP and Mg2+ for its activity and AMP is generated as a side product, suggesting that the substrate is activated by adenylation | Xanthomonas oryzae | ? | - |
? | |
| 5.1.1.23 | additional information | XOO_1319 is a distinct type of glycopeptidyl-glutamate epimerase and is designated XOO_1319 as UDP-MurNAc-LAla-L-Glu epimerase, MurL. It shows no activity in the reverse reaction with UDP-MurNAc-L-Ala-D-Glu. MurL requires ATP and Mg2+ for its activity and AMP is generated as a side product, suggesting that the substrate is activated by adenylation | Xanthomonas oryzae MAFF311018 | ? | - |
? | |
| 6.3.2.53 | ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + L-glutamate | - |
Xanthomonas oryzae | ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate | - |
? | |
| 6.3.2.53 | ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + L-glutamate | - |
Xanthomonas oryzae MAFF311018 | ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 5.1.1.20 | More | the enzyme structure comprises an N-terminal capping domain and a C-terminal (beta/alpha)7beta-barrel, and the active site is located in the barrel domain. The Mg2+ ion forms a bidentate interaction with the alpha-carbonyl group of the Glu of the substrate and the alpha-carbon center to be epimerized is located between two conserved lysine residues | Escherichia coli |
| 5.1.1.20 | More | the enzyme structure comprises an N-terminal capping domain and a C-terminal (beta/alpha)7beta-barrel, and the active site is located in the barrel domain. The Mg2+ ion forms a bidentate interaction with the alpha-carbonyl group of the Glu of the substrate and the alpha-carbon center to be epimerized is located between two conserved lysine residues, K162 and K268 in YkfB | Bacillus subtilis |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 5.1.1.20 | L-Ala-D/L-Glu epimerase | - |
Escherichia coli |
| 5.1.1.20 | L-Ala-D/L-Glu epimerase | - |
Bacillus subtilis |
| 5.1.1.20 | YcjG | - |
Escherichia coli |
| 5.1.1.20 | YfkA | - |
Bacillus subtilis |
| 5.1.1.20 | YfkB | - |
Bacillus subtilis |
| 5.1.1.23 | MurL | - |
Xanthomonas oryzae |
| 5.1.1.23 | UDP-MurNAc-L-Ala-L-Glu epimerase | - |
Xanthomonas oryzae |
| 5.1.1.23 | XOO_1319 | - |
Xanthomonas oryzae |
| 6.3.2.53 | murD2 | - |
Xanthomonas oryzae |
| 6.3.2.53 | UDP-MurNAc-L-Ala-L-Glu synthetase | - |
Xanthomonas oryzae |
| 6.3.2.53 | XOO_1320 | - |
Xanthomonas oryzae |
Cofactor
| EC Number | Cofactor | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.1.23 | ATP | - |
Xanthomonas oryzae | |
| 6.3.2.53 | ATP | - |
Xanthomonas oryzae | |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 5.1.1.20 | evolution | the enzyme belongs to the enolase superfamily enzymes. The enzyme reaction shows the common enolase family reaction mechanism: Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate. The fate of the intermediate is determined by the active site of each enzyme to produce the specific product | Escherichia coli |
| 5.1.1.20 | evolution | the enzyme belongs to the enolase superfamily enzymes. The enzyme reaction shows the common enolase family reaction mechanism: Mg2+-assisted general base-catalyzed abstraction of the alpha-proton of a carboxylic acid and stabilization of an enolate anion intermediate. The fate of the intermediate is determined by the active site of each enzyme to produce the specific product | Bacillus subtilis |
| 5.1.1.20 | physiological function | YcjG is a L-Ala-D/LGlu epimerases, which converts L-Ala-D-Glu into L-Ala-L-Glu for degradation and recycling of peptidoglycan | Escherichia coli |
| 5.1.1.20 | physiological function | YfkB is a L-Ala-D/LGlu epimerases, which converts L-Ala-D-Glu into L-Ala-L-Glu for degradation and recycling of peptidoglycan | Bacillus subtilis |
| 5.1.1.23 | metabolism | the enzyme is involved in the biosynthesis of UDP-MurNAc-pentapeptide, pathway overview | Xanthomonas oryzae |
| 5.1.1.23 | additional information | MurL lacks known conserved domains and cofactor binding domains | Xanthomonas oryzae |
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