5CGX

CRYSTAL STRUCTURE OF Fox-4 cephamycinase mutant Y150F complexed with cefoxitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

FOX-4 cephamycinase: an analysis of structure and function.

Lefurgy, S.T.Malashkevich, V.N.Aguilan, J.T.Nieves, E.Mundorff, E.C.Biju, B.Noel, M.A.Toro, R.Baiwir, D.Papp-Wallace, K.M.Almo, S.C.Frere, J.M.Bou, G.Bonomo, R.A.

(2015) Antimicrob.Agents Chemother. --: --

  • DOI: 10.1128/AAC.01887-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Class C β-lactamases poorly hydrolyze cephamycins (e.g., cefoxitin, cefotetan, and moxalactam). In the past 2 decades, a new family of plasmid-based AmpC β-lactamases conferring resistance to cefoxitin, the FOX family, has grown to include nine uniqu ...

    Class C β-lactamases poorly hydrolyze cephamycins (e.g., cefoxitin, cefotetan, and moxalactam). In the past 2 decades, a new family of plasmid-based AmpC β-lactamases conferring resistance to cefoxitin, the FOX family, has grown to include nine unique members descended from the Aeromonas caviae chromosomal AmpC. To understand the basis for the unique cephamycinase activity in the FOX family, we determined the first X-ray crystal structures of FOX-4, apo enzyme and the acyl-enzyme with its namesake compound, cefoxitin, using the Y150F deacylation-deficient variant. Notably, recombinant expression of N-terminally tagged FOX-4 also yielded an inactive adenylylated enzyme form not previously observed in β-lactamases. The posttranslational modification (PTM), which occurs on the active site Ser64, would not seem to provide a selective advantage, yet might present an opportunity for the design of novel antibacterial drugs. Substantial ligand-induced changes in the enzyme are seen in the acyl-enzyme complex, particularly the R2 loop and helix H10 (P289 to N297), with movement of F293 by 10.3 Å. Taken together, this study provides the first picture of this highly proficient class C cephamycinase, uncovers a novel PTM, and suggests a possible cephamycin resistance mechanism involving repositioning of the substrate due to the presence of S153P, N289P, and N346I substitutions in the ligand binding pocket.


    Organizational Affiliation

    Servicio de Microbiologìa, Complejo Hospitalario Universitario A. Coruña, La Coruña, Spain.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.,Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,GIGA Proteomic Facility, Mass Spectrometry Laboratory GIGA-R, Université de Liège, Sart-Tilman, Liège, Belgium.,Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA robert.bonomo@va.gov.,Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, Sart-Tilman, Liège, Belgium.,Department of Chemistry, Hofstra University, Hempstead, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
362Escherichia coliMutation(s): 1 
Gene Names: fox-4
EC: 3.5.2.6
Find proteins for Q9L387 (Escherichia coli)
Go to UniProtKB:  Q9L387
Small Molecules
Ligands 3 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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
1S7
Query on 1S7

Download SDF File 
Download CCD File 
A
(2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
Cefoxitin, bound form
C15 H16 N2 O5 S2
BMQDZZSQSZJJQV-CABCVRRESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.524α = 90.00
b = 56.588β = 99.23
c = 55.485γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release