5F83

Imipenem complex of the GES-5 C69G mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Role of the Conserved Disulfide Bridge in Class A Carbapenemases.

Smith, C.A.Nossoni, Z.Toth, M.Stewart, N.K.Frase, H.Vakulenko, S.B.

(2016) J.Biol.Chem. 291: 22196-22206

  • DOI: 10.1074/jbc.M116.749648
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Some members of the class A β-lactamase family are capable of conferring resistance to the last resort antibiotics, carbapenems. A unique structural feature of these clinically important enzymes, collectively referred to as class A carbapenemases, is ...

    Some members of the class A β-lactamase family are capable of conferring resistance to the last resort antibiotics, carbapenems. A unique structural feature of these clinically important enzymes, collectively referred to as class A carbapenemases, is a disulfide bridge between invariant Cys 69 and Cys 238 residues. It was proposed that this conserved disulfide bridge is responsible for their carbapenemase activity, but this has not yet been validated. Here we show that disruption of the disulfide bridge in the GES-5 carbapenemase by the C69G substitution results in only minor decreases in the conferred levels of resistance to the carbapenem imipenem and other β-lactams. Kinetic and circular dichroism experiments with C69G-GES-5 demonstrate that this small drop in antibiotic resistance is due to a decline in the enzyme activity caused by a marginal loss of its thermal stability. The atomic resolution crystal structure of C69G-GES-5 shows that two domains of this disulfide bridge-deficient enzyme are held together by an intensive hydrogen-bonding network. As a result, the protein architecture and imipenem binding mode remain unchanged. In contrast, the corresponding hydrogen-bonding networks in NMCA, SFC-1, and SME-1 carbapenemases are less intensive, and as a consequence, disruption of the disulfide bridge in these enzymes destabilizes them, which causes arrest of bacterial growth. Our results demonstrate that the disulfide bridge is essential for stability but does not play a direct role in the carbapenemase activity of the GES family of β-lactamases. This would likely apply to all other class A carbapenemases given the high degree of their structural similarity.


    Organizational Affiliation

    From the Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California 94025 and csmith@slac.stanford.edu.,the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556.,the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 svakulen@nd.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
268Pseudomonas aeruginosaMutation(s): 1 
Gene Names: blaGES-5
EC: 3.5.2.6
Find proteins for Q0Z8S4 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q0Z8S4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IM2
Query on IM2

Download SDF File 
Download CCD File 
A, B
(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid
IMIPENEM, open form; N-FORMIMIDOYL-THIENAMYCINE, open form
C12 H19 N3 O4 S
UACUABDJLSUFFC-IWSPIJDZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.920α = 90.00
b = 81.483β = 101.97
c = 71.716γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
Cootmodel building
XDSdata scaling
Blu-Icedata collection
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI089726

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2016-10-26
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-22
    Type: Refinement description