4FCF

K234R: apo structure of inhibitor resistant beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and exploration of novel boronic acid inhibitors reveals important interactions with a clavulanic acid-resistant sulfhydryl-variable (SHV) beta-lactamase.

Winkler, M.L.Rodkey, E.A.Taracila, M.A.Drawz, S.M.Bethel, C.R.Papp-Wallace, K.M.Smith, K.M.Xu, Y.Dwulit-Smith, J.R.Romagnoli, C.Caselli, E.Prati, F.van den Akker, F.Bonomo, R.A.

(2013) J.Med.Chem. 56: 1084-1097

  • DOI: 10.1021/jm301490d

  • PubMed Abstract: 
  • Inhibitor resistant (IR) class A β-lactamases pose a significant threat to many current antibiotic combinations. The K234R substitution in the SHV β-lactamase, from Klebsiella pneumoniae , results in resistance to ampicillin/clavulanate. After site-s ...

    Inhibitor resistant (IR) class A β-lactamases pose a significant threat to many current antibiotic combinations. The K234R substitution in the SHV β-lactamase, from Klebsiella pneumoniae , results in resistance to ampicillin/clavulanate. After site-saturation mutagenesis of Lys-234 in SHV, microbiological and biochemical characterization of the resulting β-lactamases revealed that only -Arg conferred resistance to ampicillin/clavulanate. X-ray crystallography revealed two conformations of Arg-234 and Ser-130 in SHV K234R. The movement of Ser-130 is the principal cause of the observed clavulanate resistance. A panel of boronic acid inhibitors was designed and tested against SHV-1 and SHV K234R. A chiral ampicillin analogue was discovered to have a 2.4 ± 0.2 nM K(i) for SHV K234R; the chiral ampicillin analogue formed a more complex hydrogen-bonding network in SHV K234R vs SHV-1. Consideration of the spatial position of Ser-130 and Lys-234 and this hydrogen-bonding network will be important in the design of novel antibiotics targeting IR β-lactamases.


    Organizational Affiliation

    Department of Microbiology and Molecular Biology, Case Western Reserve University, Cleveland, Ohio 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase SHV-1
A
265Klebsiella pneumoniaeMutation(s): 1 
Gene Names: bla (shv1)
EC: 3.5.2.6
Find proteins for P0AD64 (Klebsiella pneumoniae)
Go to UniProtKB:  P0AD64
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MA4
Query on MA4

Download SDF File 
Download CCD File 
A
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
 Ligand Interaction
TAU
Query on TAU

Download SDF File 
Download CCD File 
A
2-AMINOETHANESULFONIC ACID
C2 H7 N O3 S
XOAAWQZATWQOTB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MA4Ki: 2.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.631α = 90.00
b = 55.416β = 90.00
c = 83.951γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
Blu-Icedata collection
HKL-2000data scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references