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 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    1UAG

  • 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 structure of MurD in the presence of its substrate UMA has been solved to 1 ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYL-L-ALANINE/:D-GLUTAMATE LIGASEA437Escherichia coliMutation(s): 1 
Gene Names: MURD GENE
EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12))
Explore P14900 
Go to UniProtKB:  P14900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMA (Subject of Investigation/LOI)
Query on UMA
Download Ideal Coordinates CCD File 
 D [auth A]URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
C23 H36 N4 O20 P2
NTMMCWJNQNKACG-KBKUWGQMSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX		AL-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 
  • R-Value Observed: 0.190 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.428α = 90
b = 65.428β = 90
c = 134.438γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
MADSYSphasing
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2018-04-11
    Changes: Data collection