6NVT

Crystal structure of TLA-1 extended spectrum Beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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-lactamase
A, B, C, D
276Escherichia 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
H [auth A],
HB [auth D],
I [auth A],
IB [auth D],
J [auth A],
JB [auth D],
K [auth A],
KB [auth D],
LB [auth D],
MA [auth C],
MB [auth D],
NA [auth C],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth D]
BB [auth C]
CB [auth C]
DB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FB [auth C],
GA [auth B],
GB [auth C],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
PB [auth D],
Q [auth A],
QB [auth D],
R [auth A],
RB [auth D],
S [auth A],
SB [auth D],
T [auth A],
TB [auth D],
U [auth A],
UB [auth D],
V [auth A],
VB [auth D],
W [auth A],
WB [auth D],
X [auth A],
XB [auth D],
YB [auth D],
ZB [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
FA [auth B]
L [auth A]
NB [auth D]
OB [auth D]
WA [auth C]
FA [auth B],
L [auth A],
NB [auth D],
OB [auth D],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.06α = 90
b = 99.01β = 90.04
c = 99.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: Advisory, Data collection, Database references, Refinement description