Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | 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: 28.96 kDa 
• Atom Count: 2495 
• Modelled Residue Count: 263 
• Deposited Residue Count: 263 
• Unique protein chains: 1

4RVA

A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for deacylation

• PDB DOI: 10.2210/pdb4RVA/pdb

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


• Deposited: 2014-11-25 Released: 2015-03-04 
• Deposition Author(s): Stojanoski, V., Chow, D.-C., Hu, L., Sankaran, B., Gilbert, H., Prasad, B.V.V., Palzkill, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.194 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Literature

A Triple Mutant in the Omega-loop of TEM-1 beta-Lactamase Changes the Substrate Profile via a Large Conformational Change and an Altered General Base for Catalysis.

Stojanoski, V., Chow, D.C., Hu, L., Sankaran, B., Gilbert, H.F., Prasad, B.V., Palzkill, T.

(2015) J Biol Chem 290: 10382-10394

• PubMed: 25713062 
• DOI: 10.1074/jbc.M114.633438
• Primary Citation of Related Structures:  
  4RVA, 4RX2, 4RX3


• PubMed Abstract: 
  

β-Lactamases are bacterial enzymes that hydrolyze β-lactam antibiotics. TEM-1 is a prevalent plasmid-encoded β-lactamase in Gram-negative bacteria that efficiently catalyzes the hydrolysis of penicillins and early cephalosporins but not oxyimino-cephalosporins. A previous random mutagenesis study identified a W165Y/E166Y/P167G triple mutant that displays greatly altered substrate specificity with increased activity for the oxyimino-cephalosporin, ceftazidime, and decreased activity toward all other β-lactams tested. Surprisingly, this mutant lacks the conserved Glu-166 residue critical for enzyme function. Ceftazidime contains a large, bulky side chain that does not fit optimally in the wild-type TEM-1 active site. Therefore, it was hypothesized that the substitutions in the mutant expand the binding site in the enzyme. To investigate structural changes and address whether there is an enlargement in the active site, the crystal structure of the triple mutant was solved to 1.44 Å. The structure reveals a large conformational change of the active site Ω-loop structure to create additional space for the ceftazidime side chain. The position of the hydroxyl group of Tyr-166 and an observed shift in the pH profile of the triple mutant suggests that Tyr-166 participates in the hydrolytic mechanism of the enzyme. These findings indicate that the highly conserved Glu-166 residue can be substituted in the mechanism of serine β-lactamases. The results reveal that the robustness of the overall β-lactamase fold coupled with the plasticity of an active site loop facilitates the evolution of enzyme specificity and mechanism.

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Organizational Affiliation: 

From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and the Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase TEM	A	263	Escherichia coli	Mutation(s): 4  Gene Names: bla, blaT-3, blaT-4, blaT-5, blaT-6 EC: 3.5.2.6
UniProt
Find proteins for P62593 (Escherichia coli) Explore P62593  Go to UniProtKB:  P62593

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCT	B [auth A]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.194 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.045	α = 90
b = 59.505	β = 90
c = 86.26	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-25 
• Released Date: 2015-03-04 
Deposition Author(s): Stojanoski, V., Chow, D.-C., Hu, L., Sankaran, B., Gilbert, H., Prasad, B.V.V., Palzkill, T.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2015-05-06
  Changes: Database references