6NVU

Crystal structure of TLA-1 extended spectrum Beta-lactamase in complex with Clavulanic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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-lactamase277Escherichia coliMutation(s): 0 
Gene Names: tla-1
EC: 3.5.2.6
UniProt
Find proteins for Q9X6W1 (Escherichia coli)
Explore Q9X6W1 
Go to UniProtKB:  Q9X6W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6W1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L4A (Subject of Investigation/LOI)
Query on L4A

Download Ideal Coordinates CCD File 
I [auth A]2,5-bis(2-hydroxyethyl)-1,3-oxazole-4-carboxylic acid
C8 H11 N O5
PLUGCRBIUHQSBZ-UHFFFAOYSA-N
J01 (Subject of Investigation/LOI)
Query on J01

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
(2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
C8 H9 N O5
HZZVJAQRINQKSD-PBFISZAISA-N
TEM (Subject of Investigation/LOI)
Query on TEM

Download Ideal Coordinates CCD File 
F [auth A]N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE
C7 H11 N O3
FXITUJNZFYVSNC-RCYFRSRISA-N
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.64α = 90
b = 98.64β = 90
c = 100.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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, Derived calculations, Refinement description