1DLG

CRYSTAL STRUCTURE OF THE C115S ENTEROBACTER CLOACAE MURA IN THE UN-LIGANDED STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 2164-2173


  • PubMed Abstract: 
  • The induced-fit mechanism in Enterobacter cloacae MurA has been investigated by kinetic studies and X-ray crystallography. The antibiotic fosfomycin, an irreversible inhibitor of MurA, induced a structural change in UDP-N-acetylglucosamine (UDPGlcNAc ...

    The induced-fit mechanism in Enterobacter cloacae MurA has been investigated by kinetic studies and X-ray crystallography. The antibiotic fosfomycin, an irreversible inhibitor of MurA, induced a structural change in UDP-N-acetylglucosamine (UDPGlcNAc)-liganded enzyme with a time dependence similar to that observed for the inactivation progress. The mechanism of action of fosfomycin on MurA appeared to be of the bimolecular type, the overall rate constants of inactivation and structural change being = 104 M(-1) s(-1) and = 85 M(-1) s(-1), respectively. Fosfomycin as well as the second MurA substrate, phosphoenolpyruvate (PEP), are known to interact with the side chain of Cys115. Like wild-type MurA, the catalytically inactive single-site mutant protein Cys115Ser structurally interacted with UDPGlcNAc in a rapidly reversible reaction. However, in contrast to wild-type enzyme, binding of PEP to mutant protein induced a rate-limited, biphasic structural change. Fosfomycin did not affect the structure of the mutant protein. The crystal structure of unliganded Cys115Ser MurA at 1.9 A resolution revealed that the overall conformation of the loop comprising residues 112-121 is not influenced by the mutation. However, other than Cys115 in wild-type MurA, Ser115 exhibits two distinct side-chain conformations. A detailed view on the loop revealed the existence of an elaborate hydrogen-bonding network mainly supplied by water molecules, presumably stabilizing its conformation in the unliganded state. The comparison between the known crystal structures of MurA, together with the kinetic data obtained, suggest intermediate conformational states in the MurA reaction, in which the loop undergoes multiple structural changes upon ligand binding.


    Related Citations: 
    • Comparative X-ray analysis of the un-liganded fosfomycin target MurA
      Eschenburg, S.,Schonbrunn, E.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Swiss Federal Institute of Technology, Institute of Plant Sciences, Universit├Ątstrasse 2, CH-8092 Z├╝rich, Switzerland. eschoenb@lamar.colostate.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA
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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.685α = 90.00
b = 155.532β = 91.82
c = 83.820γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-12
    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
  • Version 1.4: 2011-11-16
    Type: Atomic model