6PQ9

Crystal Structure of TLA-1 S70G extended spectrum Beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of ESBL TLA-1 in complex with clavulanic acid reveals a second acylation site.

Cifuentes-Castro, V.Rodriguez-Almazan, C.Silva-Sanchez, J.Rudino-Pinera, E.

(2020) Biochem Biophys Res Commun 522: 545-551

  • DOI: https://doi.org/10.1016/j.bbrc.2019.11.138
  • Primary Citation of Related Structures:  
    6NVT, 6NVU, 6PQ8, 6PQ9

  • PubMed Abstract: 

    β-lactamases are the main molecules responsible for giving bacterial resistance against β-lactam antibiotics. The study of β-lactamases has allowed the development of antibiotics capable of inhibiting these enzymes. In this context, extended spectrum β-lactamase (ESBL) TLA-1 has spread in Escherichia coli and Enterobacter cloacae clinical isolates during the last 30 years in Mexico. In this research, the 3D structures of ESBL TLA-1 and TLA-1 S70G mutant, both ligand-free and in complex with clavulanic acid were determined by X-ray crystallography. Four clavulanic acid molecules were found in the structure of TLA-1, two of those were intermediaries of the acylation process and were localized covalently bound to two different amino acid residues, Ser70 and Ser237. The coordinates of TLA-1 in complex with clavulanic acid shows the existence of a second acylation site, additional to Ser70, which might be extendable to several members of the subclass A β-lactamases family. This is the first time that two serines involved in binding clavulanic acid has been reported and described to an atomic level.


  • Organizational Affiliation

    Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, C.P. 62210, Cuernavaca, Morelos, Mexico.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase299Escherichia coliMutation(s): 1 
Gene Names: tla-1
EC: 3.5.2.6
UniProt
Find proteins for Q9X6W1 (Escherichia coli)
Go to UniProtKB:  Q9X6W1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download Ideal Coordinates CCD File 
B [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.41α = 90
b = 99.41β = 90
c = 99.47γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description