2UAG

UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.

Bertrand, J.A.Auger, G.Martin, L.Fanchon, E.Blanot, D.Le Beller, D.van Heijenoort, J.Dideberg, O.

(1999) J.Mol.Biol. 289: 579-590

  • DOI: 10.1006/jmbi.1999.2800
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • UDP -N- acetylmuramoyl- L -alanine: D -glutamate (MurD) ligase catalyses the addition of d -glutamate to the nucleotide precursor UDP -N- acetylmuramoyl- L -alanine (UMA). The crystal structures of three complexes of Escherichia coli MurD with a vari ...

    UDP -N- acetylmuramoyl- L -alanine: D -glutamate (MurD) ligase catalyses the addition of d -glutamate to the nucleotide precursor UDP -N- acetylmuramoyl- L -alanine (UMA). The crystal structures of three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolution. These include (1) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mg2+, (2) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mn2+, and (3) the binary complex of MurD with the product UDP - N- acetylmuramoyl- L -alanine- D -glutamate (UMAG). The reaction mechanism supported by these structures proceeds by the phosphorylation of the C-terminal carboxylate group of UMA by the gamma-phosphate group of ATP to form an acyl-phosphate intermediate, followed by the nucleophilic attack by the amino group of D-glutamate to produce UMAG. A key feature in the reaction intermediate is the presence of two magnesium ions bridging negatively charged groups.


    Related Citations: 
    • Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
      Bertrand, J.A.,Auger, G.,Fanchon, E.,Martin, L.,Blanot, D.,van Heijenoort, J.,Dideberg, O.
      (1997) Embo J. 16: 3416
    • Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli.
      Auger, G.,Martin, L.,Bertrand, J.,Ferrari, P.,Fanchon, E.,Vaganay, S.,Petillot, Y.,van Heijenoort, J.,Blanot, D.,Dideberg, O.
      (1998) Protein Expr.Purif. 13: 23


    Organizational Affiliation

    Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), 41 rue Jules Horowitz, Grenoble Cedex 1, F-38027, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE)
A
437Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: murD
EC: 6.3.2.9
Find proteins for P14900 (Escherichia coli (strain K12))
Go to UniProtKB:  P14900
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UMA
Query on UMA

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
C23 H36 N4 O20 P2
NTMMCWJNQNKACG-KBKUWGQMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 65.560α = 90.00
b = 65.560β = 90.00
c = 136.010γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection
  • Version 1.4: 2018-04-11
    Type: Data collection
  • Version 1.5: 2019-11-06
    Type: Data collection, Database references, Derived calculations