6PQ8

Crystal structure of TLA-1 S70G extended spectrum Beta-lactamase in complex with clavulanic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 

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This is version 1.1 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: 10.1016/j.bbrc.2019.11.138
  • Primary Citation of Related Structures:  

  • 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-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.,Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, C.P. 62210, Cuernavaca, Morelos, Mexico. Electronic address: rudino@ibt.unam.mx.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
299Escherichia coliMutation(s): 1 
Gene Names: tla-1
EC: 3.5.2.6
Find proteins for Q9X6W1 (Escherichia coli)
Go to UniProtKB:  Q9X6W1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
J01
Query on J01

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A
(2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
CLAVULANIC ACID
C8 H9 N O5
HZZVJAQRINQKSD-PBFISZAISA-N
 Ligand Interaction
ASP
Query on ASP

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A
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.410α = 90.00
b = 99.410β = 90.00
c = 99.470γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references