6U58

Toho1 Beta Lactamase Glu166Gln Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.240 

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Literature

Probing the Role of the Conserved Residue Glu166 in a Class A Beta-Lactamase Using Neutron and X-ray Protein Crystallography

Langan, P.S.Sullivan, B.Weiss, K.L.Coates, L.

(2020) Acta Crystallogr D Biol Crystallogr 76: 118-123

  • DOI: 10.1107/S2059798319016334
  • Primary Citation of Related Structures:  
    6U58

  • PubMed Abstract: 
  • The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains ...

    The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains. To investigate the function of Glu166 in the acylation part of the catalytic mechanism, neutron and X-ray crystallographic studies were performed on a Glu166Gln mutant. The structure of this class A β-lactamase mutant provides several insights into its previously reported reduced drug-binding kinetic rates. A joint refinement of both X-ray and neutron diffraction data was used to study the effects of the Glu166Gln mutation on the active site of Toho-1. This structure reveals that while the Glu166Gln mutation has a somewhat limited impact on the positions of the conserved amino acids within the active site, it displaces the catalytic water molecule from the active site. These subtle changes offer a structural explanation for the previously observed decreases in the binding of non-β-lactam inhibitors such as the recently developed diazobicyclooctane inhibitor avibactam.


    Organizational Affiliation

    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA261Escherichia coliMutation(s): 1 
Gene Names: bla CTX-M-56bla
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.150 
  • Space Group: P 32 2 1
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.543α = 90
b = 73.543β = 90
c = 99.721γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Mantiddata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release