4QHC | pdb_00004qhc

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.207 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.biochem.5b00698
  • Primary Citation Related Structures: 
    4QHC

  • 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 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 Biotechnology, Indian Institute of Technology, Roorkee , Roorkee, Uttarakhand 247667, India.

Macromolecule Content 

  • Total Structure Weight: 28.87 kDa 
  • Atom Count: 2,236 
  • Modeled Residue Count: 265 
  • Deposited Residue Count: 266 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase266Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: blaAblaCRv2068cMTCY49.07c
EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD3 
Go to UniProtKB:  P9WKD3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKD3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
33V

Query on 33V



Download:Ideal Coordinates CCD File
B [auth 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
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.207 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.699α = 90
b = 68.33β = 90
c = 75.247γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations