5KMT

CTX-M9 mutant L48A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1039/c7sc02676e
  • Primary Citation of Related Structures:  

  • 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 resistan ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
290Escherichia coliMutation(s): 1 
Gene Names: blaCTX-M-9a (blaCTX-M-9, blaCTX-M-9b)
EC: 3.5.2.6
Find proteins for Q9L5C8 (Escherichia coli)
Go to UniProtKB:  Q9L5C8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 41.788α = 90.00
b = 41.788β = 90.00
c = 232.401γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Hartwell FoundationUnited StatesIndividual Biomedical Research Award

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-10-25
    Type: Database references, Refinement description