4Q8I

Crystal Structure of beta-lactamase from M.tuberculosis covalently complexed with Tebipenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tebipenem, a new carbapenem antibiotic, is a slow substrate that inhibits the beta-lactamase from Mycobacterium tuberculosis.

Hazra, S.Xu, H.Blanchard, J.S.

(2014) Biochemistry 53: 3671-3678

  • DOI: 10.1021/bi500339j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The genome of Mycobacterium tuberculosis contains a gene, blaC, which encodes a highly active β-lactamase (BlaC). We have previously shown that BlaC has an extremely broad spectrum of activity against penicillins and cephalosporins but weak activity ...

    The genome of Mycobacterium tuberculosis contains a gene, blaC, which encodes a highly active β-lactamase (BlaC). We have previously shown that BlaC has an extremely broad spectrum of activity against penicillins and cephalosporins but weak activity against newer carbapenems. We have shown that carbapenems such as meropenem, doripenem, and ertapenem react with the enzyme to form enzyme-drug covalent complexes that are hydrolyzed extremely slowly. In the current study, we have determined apparent Km and kcat values of 0.8 μM and 0.03 min(-1), respectively, for tebipenem, a novel carbapenem whose prodrug form, the pivalyl ester, is orally available. Tebipenem exhibits slow tight-binding inhibition at low micromolar concentrations versus the chromogenic substrate nitrocefin. FT-ICR mass spectrometry demonstrated that the tebipenem acyl-enzyme complex remains stable for greater than 90 min and exists as mixture of the covalently bound drug and the bound retro-aldol cleavage product. We have also determined the high-resolution crystal structures of the BlaC-tebipenem covalent acylated adduct (1.9 Å) with wild-type BlaC and the BlaC-tebipenem Michaelis-Menten complex (1.75 Å) with the K73A BlaC variant. These structures are compared to each other and to other carbapenem-BlaC structures.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamaseA267Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: blaAblaCRv2068cMTCY49.07c
EC: 3.5.2.6
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD3 
Go to UniProtKB:  P9WKD3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEB
Query on TEB

Download CCD File 
A
(4R,5S)-3-(1-(4,5-dihydrothiazol-2-yl)azetidin-3-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4-methyl-4,5- dihydro-1H-pyrrole-2-carboxylic acid
C16 H23 N3 O4 S2
PGCJBZBFZXWIGF-CNVPUSNMSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.925α = 90
b = 68.026β = 90
c = 75.554γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-08-27
    Changes: Database references