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Literature summary 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.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
6.3.2.13
-
 Mycobacterium leprae

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
6.3.2.13 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

EC Number Metals/Ions Comment Organism Structure
6.3.2.8 Mg2+ required Mycobacterium leprae
6.3.2.13 Mg2+ required Mycobacterium leprae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
6.3.2.8 ATP + UDP-N-acetylmuramate + L-alanine Mycobacterium leprae
-
 ADP + phosphate + UDP-N-acetylmuramoyl-L-alanine
-
 ?
6.3.2.13 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

EC Number Organism UniProt Comment Textmining
6.3.2.8 Mycobacterium leprae P57994
-
-
6.3.2.13 Mycobacterium leprae
-
-
-
6.3.2.13 Mycobacterium leprae O69557
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
6.3.2.8 ATP + UDP-N-acetyl-alpha-D-muramate + L-alanine = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine Mur ligase reaction mechanism, overview Mycobacterium leprae
a
6.3.2.13 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
6.3.2.8 ATP + UDP-N-acetylmuramate + L-alanine
-
 Mycobacterium leprae ADP + phosphate + UDP-N-acetylmuramoyl-L-alanine
-
 ?
6.3.2.13 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
-
 ?
6.3.2.13 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

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

Synonyms

EC Number Synonyms Comment Organism
6.3.2.8 MurC
-
 Mycobacterium leprae
6.3.2.13 MurE
-
 Mycobacterium leprae

Cofactor

EC Number Cofactor Comment Organism Structure
6.3.2.8 ATP
-
 Mycobacterium leprae
6.3.2.13 ATP
-
 Mycobacterium leprae

General Information

EC Number General Information Comment Organism
6.3.2.8 additional information MurC substrate binding site structures 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
6.3.2.13 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