3HVF

X-ray crystallographic structure of CTX-M-9 S70G in complex with hydrolyzed benzylpenicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural insights into substrate recognition and product expulsion in CTX-M enzymes.

Delmas, J.Leyssene, D.Dubois, D.Birck, C.Vazeille, E.Robin, F.Bonnet, R.

(2010) J.Mol.Biol. 400: 108-120

  • DOI: 10.1016/j.jmb.2010.04.062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • beta-Lactamase-mediated resistance to beta-lactam antibiotics poses a major threat to our antibiotic armamentarium. Among beta-lactamases, a significant threat comes from enzymes that hydrolyze extended-spectrum cephalosporins such as cefotaxime. Amo ...

    beta-Lactamase-mediated resistance to beta-lactam antibiotics poses a major threat to our antibiotic armamentarium. Among beta-lactamases, a significant threat comes from enzymes that hydrolyze extended-spectrum cephalosporins such as cefotaxime. Among the enzymes that exhibit this phenotype, the CTX-M family is found worldwide. These enzymes have a small active site, which makes it difficult to explain how they hydrolyze the bulky extended-spectrum cephalosporins into the binding site. We investigated noncovalent substrate recognition and product release in CTX-M enzymes using steered molecular dynamics simulation and X-ray diffraction. An arginine residue located far from the binding site favors the capture and tracking of substrates during entrance into the catalytic pocket. We show that the accommodation of extended-spectrum cephalosporins by CTX-M enzymes induced subtle changes in the active site and established a high density of electrostatic interactions. Interestingly, the product of the catalytic reaction initiates its own release because of steric hindrances and electrostatic repulsions. This suggests that there exists a general mechanism for product release for all members of the beta-lactamase family and probably for most carboxypeptidases.


    Organizational Affiliation

    CHU Clermont-Ferrand, Laboratoire de Bactériologie, Clermont-Ferrand F-63003, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CTX-M-9 extended-spectrum beta-lactamase
A, B
263Escherichia 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNK
Query on PNK

Download SDF File 
Download CCD File 
A, B
(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
Penicillin, hydroxylated form
C16 H20 N2 O5 S
HCYWNSXLUZRKJX-RWMBFGLXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.223α = 90.00
b = 106.938β = 101.76
c = 47.827γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-23
    Type: Advisory, Non-polymer description
  • Version 1.3: 2013-11-06
    Type: Database references
  • Version 1.4: 2017-11-01
    Type: Refinement description