Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.30 kDa 
• Atom Count: 2164 
• Modelled Residue Count: 261 
• Deposited Residue Count: 261 
• Unique protein chains: 1

6U58

Toho1 Beta Lactamase Glu166Gln Mutant

• PDB DOI: 10.2210/pdb6U58/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-27 Released: 2020-02-19 
• Deposition Author(s): Langan, P.S., Sullivan, B., Weiss, K.L.

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Experimental Data Snapshot

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

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

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

• PubMed: 32038042 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	261	Escherichia coli	Mutation(s): 1  Gene Names: bla CTX-M-56, bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 73.543	α = 90
b = 73.543	β = 90
c = 99.721	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Mantid	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-08-27 
• Released Date: 2020-02-19 
Deposition Author(s): Langan, P.S., Sullivan, B., Weiss, K.L.

Revision History  

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