4BD1

Neutron 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: NEUTRON DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 

wwPDB Validation

Currently 4BD1 does not have a wwPDB validation report.


This is version 1.2 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: 10.1074/jbc.M112.436238
  • Primary Citation of Related Structures:  4BD0

  • 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 diffra ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TOHO-1 BETA-LACTAMASE
A
261Escherichia coliGene Names: bla
EC: 3.5.2.6
Find proteins for Q47066 (Escherichia coli)
Go to UniProtKB:  Q47066
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BZB
Query on BZB

Download SDF File 
Download CCD File 
A
BENZO[B]THIOPHENE-2-BORONIC ACID
C8 H7 B O2 S
YNCYPMUJDDXIRH-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction

Structure Validation

Currently 4BD1 does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references
  • Version 1.2: 2017-03-22
    Type: Data collection