5KMT

CTX-M9 mutant L48A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.

Latallo, M.J.Cortina, G.A.Faham, S.Nakamoto, R.K.Kasson, P.M.

(2017) Chem Sci 8: 6484-6492

  • DOI: https://doi.org/10.1039/c7sc02676e
  • Primary Citation of Related Structures:  
    5KMT, 5KMU

  • PubMed Abstract: 

    The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and are present in the majority of drug-resistant Gram-negative bacterial infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency, while mutant crystal structures show no detectable changes from wild-type CTX-M9. We hypothesize that increased drug resistance results from changes in the conformational ensemble of an acyl intermediate in hydrolysis. Machine-learning analyses on the three top mutants identify changes to the binding-pocket conformational ensemble by which these allosteric mutations transmit their effect. These findings show how molecular simulation can predict how allosteric mutations alter active-site conformational equilibria to increase catalytic rates and thus resistance against common clinically used antibiotics.


  • Organizational Affiliation

    Department of Molecular Physiology , University of Virginia , Box 800886 , Charlottesville , VA 22908 , USA . Email: kasson@virginia.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
290Escherichia coliMutation(s): 1 
Gene Names: blaCTX-M-9ablaCTX-M-9blaCTX-M-9b
EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli)
Explore Q9L5C8 
Go to UniProtKB:  Q9L5C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L5C8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.788α = 90
b = 41.788β = 90
c = 232.401γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Hartwell FoundationUnited StatesIndividual Biomedical Research Award

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description