5NJ2

Crystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phosphate Promotes the Recovery of Mycobacterium tuberculosis beta-Lactamase from Clavulanic Acid Inhibition.

Elings, W.Tassoni, R.van der Schoot, S.A.Luu, W.Kynast, J.P.Dai, L.Blok, A.J.Timmer, M.Florea, B.I.Pannu, N.S.Ubbink, M.

(2017) Biochemistry 56: 6257-6267

  • DOI: 10.1021/acs.biochem.7b00556
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The rise of multi- and even totally antibiotic resistant forms of Mycobacterium tuberculosis underlines the need for new antibiotics. The pathogen is resistant to β-lactam compounds due to its native serine β-lactamase, BlaC. This resistance can be c ...

    The rise of multi- and even totally antibiotic resistant forms of Mycobacterium tuberculosis underlines the need for new antibiotics. The pathogen is resistant to β-lactam compounds due to its native serine β-lactamase, BlaC. This resistance can be circumvented by administration of a β-lactamase inhibitor. We studied the interaction between BlaC and the inhibitor clavulanic acid. Our data show hydrolysis of clavulanic acid and recovery of BlaC activity upon prolonged incubation. The rate of clavulanic acid hydrolysis is much higher in the presence of phosphate ions. A specific binding site for phosphate is identified in the active site pocket, both in the crystalline state and in solution. NMR spectroscopy experiments show that phosphate binds to this site with a dissociation constant of 30 mM in the free enzyme. We conclude that inhibition of BlaC by clavulanic acid is reversible and that phosphate ions can promote the hydrolysis of the inhibitor.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamaseA, B274Mycobacterium tuberculosisMutation(s): 0 
Gene Names: blaCERS027646_02769
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AE4
Query on AE4

Download CCD File 
B
3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL
C12 H26 O6
NJRFAMBTWHGSDE-UHFFFAOYSA-N
 Ligand Interaction
ETE
Query on ETE

Download CCD File 
B
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.591α = 101.28
b = 41.683β = 90.11
c = 76.841γ = 90.43
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references