1UAG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 3416-3425

  • DOI: 10.1093/emboj/16.12.3416

  • PubMed Abstract: 
  • UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal s ...

    UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal structure of MurD in the presence of its substrate UMA has been solved to 1.9 A resolution. Phase information was obtained from multiple anomalous dispersion using the K-shell edge of selenium in combination with multiple isomorphous replacement. The structure comprises three domains of topology each reminiscent of nucleotide-binding folds: the N- and C-terminal domains are consistent with the dinucleotide-binding fold called the Rossmann fold, and the central domain with the mononucleotide-binding fold also observed in the GTPase family. The structure reveals the binding site of the substrate UMA, and comparison with known NTP complexes allows the identification of residues interacting with ATP. The study describes the first structure of the UDP-N-acetylmuramoyl-peptide ligase family.


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), Laboratoire de Cristallographie Macromoléculaire, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 1.95 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 65.428α = 90.00
b = 65.428β = 90.00
c = 134.438γ = 90.00
Software Package:
Software NamePurpose
MADSYSphasing
XDSdata scaling
XDSdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    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