Information on EC 6.3.1.12 - D-aspartate ligase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
6.3.1.12
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RECOMMENDED NAME
GeneOntology No.
D-aspartate ligase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + D-aspartate + [beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n = [beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-6-N-(beta-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acid amide formation
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
peptidoglycan biosynthesis V (beta-lactam resistance)
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peptidoglycan cross-bridge biosynthesis II (E. faecium)
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SYSTEMATIC NAME
IUBMB Comments
D-aspartate:[beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n ligase (ADP-forming)
This enzyme forms part of the peptidoglycan assembly pathway of Gram-positive bacteria grown in medium containing D-Asp. Normally, the side chains the acylate the 6-amino group of the L-lysine residue contain L-Ala-L-Ala but these amino acids are replaced by D-Asp when D-Asp is included in the medium. Hybrid chains containing L-Ala-D-Asp, L-Ala-L-Ala-D-Asp or D-Asp-L-Ala are not formed [4]. The enzyme belongs in the ATP-grasp protein superfamily [3,4]. The enzyme is highly specific for D-aspartate, as L-aspartate, D-glutamate, D-alanine, D-iso-asparagine and D-malic acid are not substrates [4]. In Enterococcus faecium, the substrate D-aspartate is produced by EC 5.1.1.13, aspartate racemase [4]
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + D-aspartate + [beta-GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n
[beta-GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-6-N-(beta-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
show the reaction diagram
ATP + D-aspartate + [beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n
[beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-6-N-(beta-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
show the reaction diagram
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + D-aspartate + [beta-GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n
[beta-GlcNAc-(1,4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-6-N-(beta-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
show the reaction diagram
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the enzyme is responsible for the addition of D-aspartic acid onto the peptidoglycan precursor. specifically ligates the beta-carboxylate of D-Asp to the epsilon-amino group of L-Lys in the nucleotide precursor UDP-N-acetylmuramyl-pentapeptide
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?
ATP + D-aspartate + [beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n
[beta-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-6-N-(beta-D-Asp)-L-Lys-D-Ala-D-Ala)]n + ADP + phosphate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
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a divalent cation is required for activity. Mg2+ and Mn2+ are approximately equally effective. Optimal concentration of Mg2+ is 20 mM
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-(4-methylphenyl)-5-[5-(3-methylphenyl)-1H-pyrazol-4-yl]-1H-tetrazole
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1H-imidazol-4-yl(diphenyl)methanol
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2-amino-N,N-bis(pyridin-2-ylmethyl)oxazole-5-carboxamide
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2-amino-N,N-dibenzyl-4-methylthiazole-5-carboxamide
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2-amino-N,N-dibenzyloxazole-5-carboxamide
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2-amino-N,N-dibenzylthiazole-5-carboxamide
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2-amino-N,N-dibutyloxazole-5-carboxamide
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2-amino-N-(1H-benzo[d]imidazol-2-yl)oxazole-5-carboxamide
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2-amino-N-benzyl-N-butyloxazole-5-carboxamide
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2-amino-N-ethyl-N-(pyridin-4-ylmethyl)oxazole-5-carboxamide
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2-[2-(4-amino-1,2,5-oxadiazol-3-yl)-1H-benzimidazol-1-yl]-N-methyl-N-phenylacetamide
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2-[2-(4-amino-1,2,5-oxadiazol-3-yl)-1H-benzimidazol-1-yl]-N-phenylacetamide
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2-[2-[(methylsulfonyl)amino]-1,3-thiazol-4-yl]-N,N-bis(thiophen-2-ylmethyl)acetamide
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4-phenyl-5-(1-phenyl-1H-tetrazol-5-yl)pyrimidin-2-amine
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5-(diphenylphosphoryl)-1,3,4-thiadiazol-2-amine
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6-[(2,4-dichlorobenzyl)sulfanyl]-9H-purin-2-amine
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6-[(2,6-dichlorobenzyl)sulfanyl]-9H-purin-2-amine
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N,N-dibenzyl-9H-purin-6-amine
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N-((1H-indol-5-yl)methyl)-2-amino-N-(3,5-dibromobenzyl)oxazole-5-carboxamide
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N-((1H-indol-5-yl)methyl)-2-aminooxazole-5-carboxamide
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N-(furan-2-ylmethyl)-5-hydroxy-N-(thiophen-2-ylmethyl)pyrazine-2-carboxamide
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N-(furan-2-ylmethyl)-6-hydroxy-N-(thiophen-2-ylmethyl)pyridine-3-carboxamide
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N-benzyl-N-(2,6-dichlorobenzyl)-9H-purin-6-amine
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N-benzyl-N-(4-chlorobenzyl)-9H-purin-6-amine
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N4-(2,3-dichlorobenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-(2,4-dichlorobenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-(2,4-difluorobenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-(2,6-difluoro-3-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-(2,6-difluorobenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-(2-chloro-6-fluorobenzyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-[(2-chloropyridin-3-yl)methyl]-N4-methyl-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N4-[(5-chlorothiophen-2-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine
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N6-(1,3-benzodioxol-5-ylmethyl)-9H-purine-2,6-diamine
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N6-(2,4-dichlorobenzyl)-9H-purine-2,6-diamine
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N6-(2,4-dimethoxybenzyl)-9H-purine-2,6-diamine
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N6-(3,4-dichlorobenzyl)-9H-purine-2,6-diamine
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additional information
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screening of a series of amino-oxazoles derived from bacterial biotin carboxylase inhibitors, the compounds show low micromolar activity against D-aspartate ligase. Screening of enzyme inhibitors with 7-amino-9H-purine and 7-amino-1H-pyrazolo[3,4-d]pyrimidine scaffolds, the compounds are competitive with respect to the ATP molecule
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
D-Aspartate
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
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pH 6.5: about 40% of maximal activity, pH 8.5: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, precipitation with ammonium sulfate, stable for at least several weeks
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21 (lDE3)/pREP4 by nickel affinity chromatography, gel filtration, and ultrafiltration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
His-tagged enzyme expression in Escherichia coli strain BL21 (lDE3)/pREP4
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
medicine