5A91

15K X-ray ligand free: Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report



Literature

Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography.

Vandavasi, V.G.Weiss, K.L.Cooper, J.B.Erskine, P.T.Tomanicek, S.J.Ostermann, A.Schrader, T.E.Ginell, S.L.Coates, L.

(2016) J Med Chem 59: 474

  • DOI: 10.1021/acs.jmedchem.5b01215
  • Primary Citation of Related Structures:  
    5A90, 5A92, 5A91, 5A93

  • PubMed Abstract: 
  • The catalytic mechanism of class A β-lactamases is often debated due in part to the large number of amino acids that interact with bound β-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A ...

    The catalytic mechanism of class A β-lactamases is often debated due in part to the large number of amino acids that interact with bound β-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type β-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 β-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzyme's native machinery.


    Organizational Affiliation

    Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N/AA262Escherichia coliMutation(s): 1 
Gene Names: bla
EC: 3.5.2.6
Find proteins for E1ANH6 (Escherichia coli)
Explore E1ANH6 
Go to UniProtKB:  E1ANH6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.398α = 90
b = 72.398β = 90
c = 97.198γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 2.0: 2019-10-09
    Changes: Advisory, Atomic model, Data collection, Experimental preparation, Other