4BD0

X-ray structure of a perdeuterated Toho-1 R274N R276N double mutant Beta-lactamase in complex with a fully deuterated boronic acid (BZB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Neutron and X-Ray Crystal Structures of a Perdeuterated Enzyme Inhibitor Complex Reveal the Catalytic Proton Network of the Toho-1 Beta-Lactamase for the Acylation Reaction.

Tomanicek, S.J.Standaert, R.F.Weiss, K.L.Ostermann, A.Schrader, T.E.Ng, J.D.Coates, L.

(2013) J Biol Chem 288: 4715

  • DOI: https://doi.org/10.1074/jbc.M112.436238
  • Primary Citation of Related Structures:  
    4BD0, 4BD1

  • PubMed Abstract: 

    The mechanism by which class A β-lactamases hydrolyze β-lactam antibiotics has been the subject of intensive investigation using many different experimental techniques. Here, we report on the novel use of both neutron and high resolution x-ray diffraction to help elucidate the identity of the catalytic base in the acylation part of the catalytic cycle, wherein the β-lactam ring is opened and an acyl-enzyme intermediate forms. To generate protein crystals optimized for neutron diffraction, we produced a perdeuterated form of the Toho-1 β-lactamase R274N/R276N mutant. Protein perdeuteration, which involves replacing all of the hydrogen atoms in a protein with deuterium, gives a much stronger signal in neutron diffraction and enables the positions of individual deuterium atoms to be located. We also synthesized a perdeuterated acylation transition state analog, benzothiophene-2-boronic acid, which was also isotopically enriched with (11)B, as (10)B is a known neutron absorber. Using the neutron diffraction data from the perdeuterated enzyme-inhibitor complex, we were able to determine the positions of deuterium atoms in the active site directly rather than by inference. The neutron diffraction results, along with supporting bond-length analysis from high resolution x-ray diffraction, strongly suggest that Glu-166 acts as the general base during the acylation reaction.


  • Organizational Affiliation

    Oak Ridge National Laboratory, OakRidge, Tennessee 37831, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-LACTAMASE TOHO-1261Escherichia coli BL21Mutation(s): 2 
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
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.118 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.5α = 90
b = 72.5β = 90
c = 97.67γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 2.0: 2019-05-08
    Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Other
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description