1X8H

The Mono-Zinc Carbapenemase CphA (N220G mutant) Shows a Zn(II)- NH2 ARG Coordination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Metallo-beta-lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase CphA and its Complex with Biapenem

Garau, G.Bebrone, C.Anne, C.Galleni, M.Frere, J.M.Dideberg, O.

(2005) J.Mol.Biol. 345: 785-795

  • DOI: 10.1016/j.jmb.2004.10.070
  • Primary Citation of Related Structures:  1X8G, 1X8I
  • Also Cited By: 2FM6, 2FU6, 2FU7, 2FU8, 2FU9, 2GKL, 2QDT

  • PubMed Abstract: 
  • One strategy developed by bacteria to resist the action of beta-lactam antibiotics is the expression of metallo-beta-lactamases. CphA from Aeromonas hydrophila is a member of a clinically important subclass of metallo-beta-lactamases that have only o ...

    One strategy developed by bacteria to resist the action of beta-lactam antibiotics is the expression of metallo-beta-lactamases. CphA from Aeromonas hydrophila is a member of a clinically important subclass of metallo-beta-lactamases that have only one zinc ion in their active site and for which no structure is available. The crystal structures of wild-type CphA and its N220G mutant show the structural features of the active site of this enzyme, which is modeled specifically for carbapenem hydrolysis. The structure of CphA after reaction with a carbapenem substrate, biapenem, reveals that the enzyme traps a reaction intermediate in the active site. These three X-ray structures have allowed us to propose how the enzyme recognizes carbapenems and suggest a mechanistic pathway for hydrolysis of the beta-lactam. This will be relevant for the design of metallo-beta-lactamase inhibitors as well as of antibiotics that escape their hydrolytic activity.


    Related Citations: 
    • The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold
      Carfi, A.,Pares, S.,Duee, E.,Galleni, M.,Duez, C.,Frere, J.M.,Dideberg, O.
      (1995) Embo J. 14: 4914
    • Update of the standard numbering scheme for class B beta-lactamases
      Garau, G.,Garcia-Saez, I.,Bebrone, C.,Anne, C.,Mercuri, P.,Galleni, M.,Frere, J.M.,Dideberg, O.
      (2004) Antimicrob.Agents Chemother. 48: 2347
    • Guanidine is a Zn(2+)-binding ligand at neutral pH in aqueous solution
      Aoki, S.,Iwaida, K.,Hanamoto, N.,Shiro, M.,Kimura, E.
      (2002) J.Am.Chem.Soc. 124: 5256


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel (CNRS-CEA-UJF), 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
228Aeromonas hydrophilaGene Names: cphA
EC: 3.5.2.6
Find proteins for P26918 (Aeromonas hydrophila)
Go to UniProtKB:  P26918
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 42.683α = 90.00
b = 101.286β = 90.00
c = 117.820γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
CCP4data scaling
CCP4phasing
MOSFLMdata reduction
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2016-02-17
    Type: Derived calculations