4GNU

Crystal structure of GES-5 carbapenemase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for progression toward the carbapenemase activity in the GES family of beta-lactamases.

Smith, C.A.Frase, H.Toth, M.Kumarasiri, M.Wiafe, K.Munoz, J.Mobashery, S.Vakulenko, S.B.

(2012) J.Am.Chem.Soc. 134: 19512-19515

  • DOI: 10.1021/ja308197j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbapenem antibiotics have become therapeutics of last resort for the treatment of difficult infections. The emergence of class-A β-lactamases that have the ability to inactivate carbapenems in the past few years is a disconcerting clinical developm ...

    Carbapenem antibiotics have become therapeutics of last resort for the treatment of difficult infections. The emergence of class-A β-lactamases that have the ability to inactivate carbapenems in the past few years is a disconcerting clinical development in light of the diminished options for treatment of infections. A member of the GES-type β-lactamase family, GES-1, turns over imipenem poorly, but the GES-5 β-lactamase is an avid catalyst for turnover of this antibiotic. We report herein high-resolution X-ray structures of the apo GES-5 β-lactamase and the GES-1 and GES-5 β-lactamases in complex with imipenem. The latter are the first structures of native class-A carbapenemases with a clinically used carbapenem antibiotic in the active site. The structural information is supplemented by information from molecular dynamics simulations, which collectively for the first time discloses how the second step of catalysis by these enzymes, namely, hydrolytic deacylation of the acyl-enzyme species, takes place effectively in the case of the GES-5 β-lactamase and significantly less so in GES-1. This information illuminates one evolutionary path that nature has taken in the direction of the inexorable emergence of resistance to carbapenem antibiotics.


    Organizational Affiliation

    Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California 94025, United States. csmith@slac.stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase GES-5
A, B
287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaGES-5
EC: 3.5.2.6
Find proteins for A0EL75 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0EL75
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.660α = 90.00
b = 80.470β = 101.48
c = 71.230γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
MOLREPphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release