5G18

Direct Observation of Active-site Protonation States in a Class A beta lactamase with a monobactam substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

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This is version 2.1 of the entry. See complete history


Literature

Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A beta-Lactamase with a Monobactam Substrate.

Vandavasi, V.G.Langan, P.S.Weiss, K.L.Parks, J.M.Cooper, J.B.Ginell, S.L.Coates, L.

(2017) Antimicrob Agents Chemother 61

  • DOI: https://doi.org/10.1128/AAC.01636-16
  • Primary Citation of Related Structures:  
    5G18, 5KSC

  • PubMed Abstract: 

    The monobactam antibiotic aztreonam is used to treat cystic fibrosis patients with chronic pulmonary infections colonized by Pseudomonas aeruginosa strains expressing CTX-M extended-spectrum β-lactamases. The protonation states of active-site residues that are responsible for hydrolysis have been determined previously for the apo form of a CTX-M β-lactamase but not for a monobactam acyl-enzyme intermediate. Here we used neutron and high-resolution X-ray crystallography to probe the mechanism by which CTX-M extended-spectrum β-lactamases hydrolyze monobactam antibiotics. In these first reported structures of a class A β-lactamase in an acyl-enzyme complex with aztreonam, we directly observed most of the hydrogen atoms (as deuterium) within the active site. Although Lys 234 is fully protonated in the acyl intermediate, we found that Lys 73 is neutral. These findings are consistent with Lys 73 being able to serve as a general base during the acylation part of the catalytic mechanism, as previously proposed.


  • Organizational Affiliation

    Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE CTX-M-97262Escherichia coliMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli)
Explore Q47066 
Go to UniProtKB:  Q47066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47066
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.445α = 90
b = 72.445β = 90
c = 97.611γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other
  • Version 2.1: 2024-10-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary