6.3.2.9: UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
This is an abbreviated version!
For detailed information about UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase, go to the full flat file.
Word Map on EC 6.3.2.9
Reaction
Synonyms
D-Glutamate-adding enzyme, D-glutamic acid adding enzyme, D-Glutamic acid-adding enzyme, MurD, MurD cell wall enzyme, MurD ligase, Synthetase, uridine diphospho-N-acetylmuramoylalanyl-D-glutamate, UDP-Mur-Nac-L-Ala:L-Glu ligase, UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase, UDP-N-acetylmuramoyl-L-alanine:D-glutamateligase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase, UDPMurNAc-L-alanine:D-glutamate ligase (ADP-forming), Uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase, Uridine diphospho-N-acetylmuramoylalanyl-D-glutamate synthetase
ECTree
6.3.2.9 UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligaseAdvanced search results
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results (Crystallization
Crystallization on EC 6.3.2.9 - UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
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CRYSTALLIZATION (Commentary) 
ORGANISM
UNIPROT
LITERATURE
crystal structure of the complexes: MurD-UDP-N-acetylmurmoly-L-alanine -Mg2+ ADP, MurD-UDP-N-acetylmurmoly-L-alanine-D-glutamate and MurD-UDP-N-acetylmurmoly-L-alanine -Mn2+ ADP
crystal structure of the enzyme in presence of its substrate UDP-N-acetylmuramoyl-L-Ala, at 1.9 A resolution
crystal structure of the open enzyme where the C-terminal domain is rotated away from the N-terminal and central domains
crystal structure of the open enzyme where the C-terminal domain is rotated away from the N-terminal and central domains, complexed with UDP-N-acetylmurmoly-L-alanine
in complex with inhibitor 4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid. Only one stereoisomer is seen in the co-crystal structure. The absolute configuration of the crystallised compound is (1R,3R,4S).The carboxyl groups at positions 1 and 3 of the rigid cyclohexyl mimetic of D-glutamic acid occupy exactly the same position as the carboxyl groups of the product UDP-MurNAc-L-Ala-D-Glu. The carboxyl group at position 3 of the cyclohexyl ring of the inhibitor forms a charge-based interaction with N of Lys348, and is additionally hydrogen-bonded with a conserved water molecule, W38, which is further hydrogen-bonded to Ogamma of Thr321 and the carboxyl group of Asp182. The carboxyl group at position 1 of the cyclohexyl ring is held in place by hydrogen bonds with Ogamma of Ser415 and the backbone nitrogen of Phe422. The sulfonic group makes hydrogen bonds with His183 and water molecules W183, W242 and W415
purified free MurD and MurD complexed with the tetrahedral reaction intermediate, hanging drop vapor diffusion method, for free enzyme crystals: mixing of 0.002 ml of 3 mg/ml protein in 20 mM HEPES, pH 5.6, 1 mM DTT, and 1 mM NaN3, with 0.002 ml of reservoir solution containing 1.8 M (NH4)2SO4, 7% v/v 2-methyl-2,4-pentanediol, and 0.1 MMES, pH 5.6, 15°C, 48 h, for complexed enzyme crystals: mixing of 0.002 ml of 4 mg/ml protein in 20 mM HEPES, pH 7.4, 1 mM DTT, 1 mM NaN3, 5 mMAMP-PNP, and 1 mM UDP-N-acetyl-alpha-D-muramoyl-L-alanine, with 0.002 ml of reservoir solution containing 1.8 M Na-malonate, pH 7.0, 15°C, 48 h, X-ray diffraction structure determination and analysis at 1.84-1.90 A resolution
structure of MurD in complex with (R,Z)-2-(3-((4-((2,4-dioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
vapour-diffusion method and hanging-drop system, high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid or N-(6-butoxy-naphthalene-2-sulfonyl)-Lglutamic acid
generation of MurD 3D models using crystal structures of PDB entries 1EEH and 2JFF as templates in Modeller9v7
