4EV4

Crystal structure of serratia fonticola carbapenemase SFC-1 E166A mutant with the acylenzyme intermediate of meropenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The basis for carbapenem hydrolysis by class A beta-lactamases: a combined investigation using crystallography and simulations.

Fonseca, F.Chudyk, E.I.van der Kamp, M.W.Correia, A.Mulholland, A.J.Spencer, J.

(2012) J.Am.Chem.Soc. 134: 18275-18285

  • DOI: 10.1021/ja304460j
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DMH

  • PubMed Abstract: 
  • Carbapenems are the most potent β-lactam antibiotics and key drugs for treating infections by Gram-negative bacteria. In such organisms, β-lactam resistance arises principally from β-lactamase production. Although carbapenems escape the activity of m ...

    Carbapenems are the most potent β-lactam antibiotics and key drugs for treating infections by Gram-negative bacteria. In such organisms, β-lactam resistance arises principally from β-lactamase production. Although carbapenems escape the activity of most β-lactamases, due in the class A enzymes to slow deacylation of the covalent acylenzyme intermediate, carbapenem-hydrolyzing class A β-lactamases are now disseminating in clinically relevant bacteria. The reasons why carbapenems are substrates for these enzymes, but inhibit other class A β-lactamases, remain to be fully established. Here, we present crystal structures of the class A carbapenemase SFC-1 from Serratia fonticola and of complexes of its Ser70 Ala (Michaelis) and Glu166 Ala (acylenzyme) mutants with the carbapenem meropenem. These are the first crystal structures of carbapenem complexes of a class A carbapenemase. Our data reveal that, in the SFC-1 acylenzyme complex, the meropenem 6α-1R-hydroxyethyl group interacts with Asn132, but not with the deacylating water molecule. Molecular dynamics simulations indicate that this mode of binding occurs in both the Michaelis and acylenzyme complexes of wild-type SFC-1. In carbapenem-inhibited class A β-lactamases, it is proposed that the deacylating water molecule is deactivated by interaction with the carbapenem 6α-1R-hydroxyethyl substituent. Structural comparisons with such enzymes suggest that in SFC-1 subtle repositioning of key residues (Ser70, Ser130, Asn132 and Asn170) enlarges the active site, permitting rotation of the carbapenem 6α-1R-hydroxyethyl group and abolishing this contact. Our data show that SFC-1, and by implication other such carbapenem-hydrolyzing enzymes, uses Asn132 to orient bound carbapenems for efficient deacylation and prevent their interaction with the deacylating water molecule.


    Organizational Affiliation

    School of Cellular and Molecular Medicine, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom. maria.fonseca@ibmc.up.pt




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbapenem-hydrolizing beta-lactamase SFC-1
A
283Serratia fonticolaMutation(s): 1 
EC: 3.5.2.6
Find proteins for Q6JP75 (Serratia fonticola)
Go to UniProtKB:  Q6JP75
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MER
Query on MER

Download SDF File 
Download CCD File 
A
(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid
Meropenem, bound form
C17 H27 N3 O5 S
DYQHXZPAIVAJRU-HTXLXMOSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HAR
Query on HAR
A
L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.185α = 90.00
b = 61.955β = 90.00
c = 79.127γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references