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6.3.2.13: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

This is an abbreviated version!
For detailed information about UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase, go to the full flat file.

Word Map on EC 6.3.2.13

Reaction

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

Synonyms

amide ligase, Diaminopimelic-adding enzyme, mDAP ligase, Meso-diaminopimelate-adding enzyme, Mur ligase, MurE, MurE synthetase, MurEEr, peptidoglycan MurE ligase, Synthetase, uridine diphospho-N-acetylmuramoylalanyl-D-glutamyl-meso-2,6-diaminopimelate, UDP-MurNAc-tripeptide synthetase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase, UDP-N-acetylmuramyl tripeptide synthetase, UDP-N-acetylmuramyl-tripeptide synthetase, UDPMurNAc-L-alanyl-D-glutamate:mDAP ligase (ADP-forming), Uridine diphosphate N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase, Uridine-diphosphate-N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate synthetase

ECTree

     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.2 Acid—amino-acid ligases (peptide synthases)
                6.3.2.13 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

Crystallization

Crystallization on EC 6.3.2.13 - UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of native and selenomethionine MurE are grown in the presence of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate, 0.002 ml of protein solution containing 10 mg/ml enzyme, 20 mM HEPES, pH 7.5 200 mM NaCl, 5 mM dithiothreitol and 1 mM UDP-N-acetylmuramoyl-L-alanyl-D-glutamate, are equilibrated together with 0.002 ml reservoir buffer consisting of 100 mM HEPES, pH 7.5, 13% polyethylene glycol monomethyl ether 5000, 500 mM LiCl, 10% isopropanol and 5 mM dithiothreitol, against 1 ml reservoir buffer, crystals diffract to 2.0 A
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
computational docking of inhibitors to crystal structure. Uracil recognition site is a probable binding site for quinolone inhibitors
-
to 3.0 A resolution in the presence of the substrate UDP-MurNAc-L-Ala-D-Glu. Protein consists of 3 domains consisting of residues 25-139,140-378 and 379-535, respectively. The UAG ligand binds to both domains 1 and 2 with the UDP portion binding to domain 1 and the peptide to domain 2. The substrate molecule UAG is bound between domains 1 and 2