Literature summary for 6.3.2.13 extracted from

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 (2012), J. Mol. Model., 18, 115-125.

Cloned(Commentary)

Cloned (Comment)	Organism
-	Mycobacterium leprae

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Mycobacterium leprae

Crystallization (Comment)

Organism

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

Mycobacterium leprae

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Mycobacterium leprae

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate	Mycobacterium leprae	-	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate	-	?

Organism

Organism	UniProt	Comment	Textmining
Mycobacterium leprae	-	-	-
Mycobacterium leprae	O69557	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
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	Mur ligase reaction mechanism, overview	Mycobacterium leprae	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + UDP-MurNAc-L-Ala-D-Glu + meso-2,6-diaminoheptanedioate	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	Mycobacterium leprae	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate	-	?
ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate	-	Mycobacterium leprae	ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate	-	?

Subunits

Subunits	Comment	Organism
More	MurE domain structure and three-dimensional structure modeling by homology modeling method, structure comparisons of Mur ligases overview	Mycobacterium leprae

Synonyms

Synonyms	Comment	Organism
MurE	-	Mycobacterium leprae

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Mycobacterium leprae

General Information

General Information	Comment	Organism
additional information	MurE substrate binding sitestructures and three-dimensional structure modeling by homology modeling method, structure comparisons of Mur ligases, detailed overview. Identification of residues playing an important role in the catalytic activity of each of the Mur enzymes, docking of enzyme and substrate and ATP	Mycobacterium leprae