1EJD

Crystal structure of unliganded mura (type1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Comparative X-ray analysis of the un-liganded fosfomycin-target murA.

Eschenburg, S.Schonbrunn, E.

(2000) Proteins 40: 290-298

  • Primary Citation of Related Structures:  1EJC

  • PubMed Abstract: 
  • MurA, an essential enzyme for the synthesis of the bacterial cell wall, follows an induced-fit mechanism. Upon substrate binding, the active site forms in the interdomain cleft, involving movements of the two domains of the protein and a reorientatio ...

    MurA, an essential enzyme for the synthesis of the bacterial cell wall, follows an induced-fit mechanism. Upon substrate binding, the active site forms in the interdomain cleft, involving movements of the two domains of the protein and a reorientation of the loop Pro112-Pro121. We compare two structures of un-liganded MurA from Enterobacter cloacae: a new orthorhombic form, solved to 1.80 A resolution, and a monoclinic form, redetermined to 1.55 A resolution. In the monoclinic form, the loop Pro112-Pro121 stretches into solvent, while in the new form it adopts a winded conformation, thereby reducing solvent accessibility of the critical residue Cys115. In the interdomain cleft a network of 27 common water molecules has been identified, which partially shields negative charges in the cleft and stabilizes the orientation of catalytically crucial residues. This could support substrate binding and ease domain movements. Near the hinge region an isoaspartyl residue has been recognized, which is the product of post-translational modification of the genetically encoded Asn67-Gly68. The homogeneous population with L-isoaspartate in both structures suggests that the modification in Enterobacter cloacae MurA is not a mere aging defect but rather the result of a specific in vivo process.


    Related Citations: 
    • Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin
      Schonbrunn, E.,Sack, S.,Eschenburg, S.,Perrakis, A.,Krekel, F.,Amrhein, N.,Mandelkow, E.
      (1996) Structure 4: 1065
    • Role of the Loop Containing Residue 115 in the Induced-fit Mechanism of the Bacterial Cell Wall Biosynthetic Enzyme MurA
      Schonbrunn, E.,Eschenburg, S.,Krekel, F.,Luger, K.,Amrhein, N.
      (2000) Biochemistry 39: 2164


    Organizational Affiliation

    Max-Planck-Institute for Medical Research, Department of Biophysics, Heidelberg, Germany. seschen@mpimf-heidelberg.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
A, B
419Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56)Gene Names: murA (murZ)
EC: 2.5.1.7
Find proteins for P33038 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56))
Go to UniProtKB:  P33038
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HAI
Query on HAI

Download SDF File 
Download CCD File 
A, B
CYCLOHEXYLAMMONIUM ION
C6 H14 N
PAFZNILMFXTMIY-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IAS
Query on IAS
A, B
L-beta-peptide, C-gamma linkingC4 H7 N O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.177α = 90.00
b = 156.297β = 91.63
c = 84.036γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description