4QHC

Structure of M.Tuberculosis Betalactamase (Blac) with inhibitor having novel mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kinetic and Structural Characterization of the Interaction of 6-Methylidene Penem 2 with the beta-Lactamase from Mycobacterium tuberculosis.

Hazra, S.Kurz, S.G.Wolff, K.Nguyen, L.Bonomo, R.A.Blanchard, J.S.

(2015) Biochemistry 54: 5657-5664

  • DOI: 10.1021/acs.biochem.5b00698

  • PubMed Abstract: 
  • Mycobacterium tuberculosis is intrinsically resistant to most β-lactam antibiotics because of the constitutive expression of the blaC-encoded β-lactamase. This enzyme has extremely high activity against penicillins and cephalosporins, but weaker acti ...

    Mycobacterium tuberculosis is intrinsically resistant to most β-lactam antibiotics because of the constitutive expression of the blaC-encoded β-lactamase. This enzyme has extremely high activity against penicillins and cephalosporins, but weaker activity against carbapenems. The enzyme can be inhibited by clavulanate, avibactam, and boronic acids. In this study, we investigated the ability of 6-methylidene β-lactams to inhibit BlaC. One such compound, penem 2, inhibited BlaC more than 70 times more efficiently than clavulanate. The compound forms a covalent complex with BlaC as shown by mass spectrometry. Crystallization of the complex revealed that the bound inhibitor was covalently attached via the Ser70 active site residue and that the covalently, acylated form of the inhibitor had undergone additional chemistry yielding a 4,7-thiazepine ring in place of the β-lactam and a thiazapyroline ring generated as a result of β-lactam ring opening. The stereochemistry of the product of the 7-endo-trig cyclization was the opposite of that observed previously for class A and D β-lactamases. Addition of penem 2 greatly synergized the antibacterial properties of both ampicillin and meropenem against a growing culture of M. tuberculosis. Strikingly, penem 2 alone showed significant growth inhibition, suggesting that in addition to its capability of efficiently inhibiting BlaC, it also inhibited the peptidoglycan cross-linking transpeptidases.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.,Tufts University School of Medicine , 800 Washington Street, #257, Boston, Massachusetts 02111, United States.,Early Discovery, Infectious Diseases Antibacterial & Antifungal, Merck Research Laboratories , Kenilworth, New Jersey 07033, United States.,Department of Biotechnology, Indian Institute of Technology, Roorkee , Roorkee, Uttarakhand 247667, India.,Department of Medicine, Louis Stokes Cleveland Veterans Affairs Medical Center , Cleveland, Ohio 44106, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
266Mycobacterium 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
33V
Query on 33V

Download SDF File 
Download CCD File 
A
(3R,6R,7S)-7-[(2R,3aR)-hexahydropyrazolo[1,5-c][1,3]thiazin-2-yl]-6-(hydroxymethyl)-1,4-thiazepane-3-carboxylic acid
C13 H23 N3 O3 S2
BYDOKGBTKWANQM-LVEVGFFFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.699α = 90.00
b = 68.330β = 90.00
c = 75.247γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-3000data collection
PHENIXphasing
HKL-3000data reduction
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references