2YNT

GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa GIM- 1: active site plasticity in metallo-beta-lactamases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.598 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases.

Borra, P.S.Samuelsen, O.Spencer, J.Walsh, T.R.Lorentzen, M.S.Leiros, H.-K.S.

(2013) Antimicrob.Agents Chemother. 57: 848

  • DOI: 10.1128/AAC.02227-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metallo-β-lactamases (MBLs) have rapidly disseminated worldwide among clinically important Gram-negative bacteria and have challenged the therapeutic use of β-lactam antibiotics, particularly carbapenems. The bla(GIM-1) gene, encoding one such enzyme ...

    Metallo-β-lactamases (MBLs) have rapidly disseminated worldwide among clinically important Gram-negative bacteria and have challenged the therapeutic use of β-lactam antibiotics, particularly carbapenems. The bla(GIM-1) gene, encoding one such enzyme, was first discovered in a Pseudomonas aeruginosa isolate from 2002 and has more recently been reported in Enterobacteriaceae. Here, we present crystal structures of GIM-1 in the apo-zinc (metal-free), mono-zinc (where Cys221 was found to be oxidized), and di-zinc forms, providing nine independently refined views of the enzyme. GIM-1 is distinguished from related MBLs in possessing a narrower active-site groove defined by aromatic side chains (Trp228 and Tyr233) at positions normally occupied by hydrophilic residues in other MBLs. Our structures reveal considerable flexibility in two loops (loop 1, residues 60 to 66; loop 2, residues 223 to 242) adjacent to the active site, with open and closed conformations defined by alternative hydrogen-bonding patterns involving Trp228. We suggest that this capacity for rearrangement permits GIM-1 to hydrolyze a wide range of β-lactams in spite of possessing a more constrained active site. Our results highlight the structural diversity within the MBL enzyme family.


    Organizational Affiliation

    Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GIM-1 PROTEIN
A, C
233Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaGIM-1 (blaGim-1)
Find proteins for Q704V1 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q704V1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GIM-1 PROTEIN
B
233Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaGIM-1 (blaGim-1)
Find proteins for Q704V1 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q704V1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.598 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.922α = 90.00
b = 140.658β = 90.00
c = 41.069γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata 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