3CG5

Crystal Structure of the Covalent Adduct Formed between TB B-lactamase and Clavulanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the covalent adduct formed between Mycobacterium tuberculosis beta-lactamase and clavulanate.

Tremblay, L.W.Hugonnet, J.E.Blanchard, J.S.

(2008) Biochemistry 47: 5312-5316

  • DOI: 10.1021/bi8001055

  • PubMed Abstract: 
  • The intrinsic resistance of Mycobacterium tuberculosis to the beta-lactam class of antibiotics arises from a chromosomally encoded, extended spectrum, class A beta-lactamase, BlaC. Herein, we report the X-ray crystallographic structure of BlaC inhibi ...

    The intrinsic resistance of Mycobacterium tuberculosis to the beta-lactam class of antibiotics arises from a chromosomally encoded, extended spectrum, class A beta-lactamase, BlaC. Herein, we report the X-ray crystallographic structure of BlaC inhibited with clavulanate at a resolution of 1.7 A with an R-factor value of 0.180 and R-free value of 0.212 for the m/ z +154 clavulanate-derived fragment observed in the active site. Structural evidence reveals the presence of hydrogen bonds to the C1 carbonyl along with a coplanar arrangement of C1, C2, C3, and N4, which favors enolization to generate a trans-alpha,beta-eneamine, stabilizing the +154 adduct from hydrolysis. The irreversible inhibition of BlaC suggests that treatment of M. tuberculosis with a combination of a beta-lactam antibiotic and clavulanate may lead to rapid bactericidal activity.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park AVenue, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
265Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: blaC (blaA)
EC: 3.5.2.6
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKD3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ISS
Query on ISS

Download SDF File 
Download CCD File 
A
(2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal
C7 H11 N O3
WWFGWBHKRFILGQ-HNQUOIGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.666α = 90.00
b = 67.655β = 90.00
c = 75.032γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CBASSdata collection
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance