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Information on EC 6.3.2.13 - UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase and Organism(s) Mycobacterium leprae and UniProt Accession O69557

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IUBMB Comments
Involved in the synthesis of a cell-wall peptide in bacteria. This enzyme adds diaminopimelate in Gram-negative organisms and in some Gram-positive organisms; in others EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---L-lysine ligase) adds lysine instead. It is the amino group of the L-centre of the diaminopimelate that is acylated.
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This record set is specific for:
Mycobacterium leprae
UNIPROT: O69557
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The taxonomic range for the selected organisms is: Mycobacterium leprae
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
mur ligase, amide ligase, meso-diaminopimelate-adding enzyme, udp-n-acetylmuramyl tripeptide synthetase, udp-n-acetylmuramoyl-l-alanyl-d-glutamate-2,6-diaminopimelate ligase, mure synthetase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Diaminopimelic-adding enzyme
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mDAP ligase
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Meso-diaminopimelate-adding enzyme
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MurE synthetase
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Synthetase, uridine diphospho-N-acetylmuramoylalanyl-D-glutamyl-meso-2,6-diaminopimelate
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UDP-MurNAc-tripeptide synthetase
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UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase
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UDP-N-acetylmuramyl-tripeptide synthetase
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UDPMurNAc-L-alanyl-D-glutamate:mDAP ligase (ADP-forming)
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Uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase
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Uridine-diphosphate-N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate synthetase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate
show the reaction diagram
Mur ligase reaction mechanism, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylic acid amide formation
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carboxamide formation
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:(L)-meso-2,6-diaminoheptanedioate gamma-ligase (ADP-forming)
Involved in the synthesis of a cell-wall peptide in bacteria. This enzyme adds diaminopimelate in Gram-negative organisms and in some Gram-positive organisms; in others EC 6.3.2.7 (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate---L-lysine ligase) adds lysine instead. It is the amino group of the L-centre of the diaminopimelate that is acylated.
CAS REGISTRY NUMBER
COMMENTARY hide
9075-09-6
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate
show the reaction diagram
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?
ATP + UDP-MurNAc-L-Ala-D-Glu + meso-2,6-diaminoheptanedioate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate
show the reaction diagram
the threedimensional structure of MurE from Mycobacterium leprae is modeled using comparative modeling methods based on the X-ray crystal structure of MurE from Escherichia coli. The docked complexes reveal the amino acids responsible for binding the substrates. Superposition of these complex structures suggests that carboxylic acid group of UDP-Nacetyl muramoyl-glycyl-D-glutamate is positioned in proximity to gamma-phosphate of the ATP to facilitate the formation of acylphosphate intermediate. The orientation of an amino group of meso-diaminopimelic acid facilitates the nucleophilic attack to form the product
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate
ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate
show the reaction diagram
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
modeling of the threedimensional structure using comparative modeling methods based on the X-ray crystal structure of MurE from Escherichia coli. The 3D-structure was docked with its substrates meso-diaminopimelic acid and UDP-N-acetylmuramoyl-glycyl-D-glutamate and its product UDP-N-acetyl muramoyl-glycyl-D-Glu-meso-diaminopimelate and also with ATP. The carboxylic acid group of UDP-N-acetylmuramoyl-glycyl-D-glutamate is positioned in proximity to gamma-phosphate of the ATP to facilitate the formation of acylphosphate intermediate. The orientation of an amino group of diaminopimelate facilitates the nucleophilic attack to form the product
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shanmugam, A.; Natarajan, J.
Comparative modeling of UDP-N-acetylmuramoyl-glycyl-D-glutamate-2,6-diaminopimelate ligase from Mycobacterium leprae and analysis of its binding features through molecular docking studies
J. Mol. Model.
18
115-125
2012
Mycobacterium leprae, Mycobacterium leprae (O69557)
Manually annotated by BRENDA team