1E8C

Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of Udp-N-Acetylmuramoyl-L-Alanyl-D-Glutamate: Meso-Diaminopimelate Ligase from Escherichia Coli

Gordon, E.J., Flouret, B., Chantalat, L., Van Heijenoort, J., Mengin-Lecreulx, D., Dideberg, O.

(2001) J Biol Chem 276: 10999

  • DOI: 10.1074/jbc.M009835200
  • Primary Citation of Related Structures:  
    1E8C

  • PubMed Abstract: 

    • UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-diaminopimelate ligase is a cytoplasmic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucleotide precursor UDP-N-acetylmuramoyl-l-alanyl-d-glutamate in the biosynthesis of bacterial cell-wall peptidoglycan ...

    UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-diaminopimelate ligase is a cytoplasmic enzyme that catalyzes the addition of meso-diaminopimelic acid to nucleotide precursor UDP-N-acetylmuramoyl-l-alanyl-d-glutamate in the biosynthesis of bacterial cell-wall peptidoglycan. The crystal structure of the Escherichia coli enzyme in the presence of the final product of the enzymatic reaction, UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, has been solved to 2.0 A resolution. Phase information was obtained by multiwavelength anomalous dispersion using the K shell edge of selenium. The protein consists of three domains, two of which have a topology reminiscent of the equivalent domain found in the already established three-dimensional structure of the UDP-N-acetylmuramoyl-l-alanine: D-glutamate-ligase (MurD) ligase, which catalyzes the immediate previous step of incorporation of d-glutamic acid in the biosynthesis of the peptidoglycan precursor. The refined model reveals the binding site for UDP-MurNAc-l-Ala-gamma-d-Glu-meso-A(2)pm, and comparison with the six known MurD structures allowed the identification of residues involved in the enzymatic mechanism. Interestingly, during refinement, an excess of electron density was observed, leading to the conclusion that, as in MurD, a carbamylated lysine residue is present in the active site. In addition, the structural determinant responsible for the selection of the amino acid to be added to the nucleotide precursor was identified.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASEA, B498Escherichia coliMutation(s): 0 
Gene Names: murE
EC: 6.3.2.13
UniProt
Find proteins for P22188 (Escherichia coli (strain K12))
Explore P22188 
Go to UniProtKB:  P22188
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UAG
Query on UAG
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
C28 H43 N5 O23 P2
OJZCATPXPWFLHF-HPUCEMLMSA-N		 Ligand Interaction
API
Query on API
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		2,6-DIAMINOPIMELIC ACID
C7 H14 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX		A, B L-PEPTIDE LINKINGC7 H14 N2 O4LYS
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.465α = 90
b = 99.69β = 90
c = 236.146γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
XDSdata reduction
SCALEPACKdata scaling
SCALAdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations, Experimental preparation, Other