3DBO

Crystal structure of a member of the VapBC family of toxin-antitoxin systems, VapBC-5, from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and Proposed Activity of a Member of the VapBC Family of Toxin-Antitoxin Systems: VapBC-5 FROM MYCOBACTERIUM TUBERCULOSIS.

Miallau, L.Faller, M.Chiang, J.Arbing, M.Guo, F.Cascio, D.Eisenberg, D.

(2009) J Biol Chem 284: 276-283

  • DOI: 10.1074/jbc.M805061200
  • Primary Citation of Related Structures:  
    3DBO

  • PubMed Abstract: 
  • In prokaryotes, cognate toxin-antitoxin pairs have long been known, but no three-dimensional structure has been available for any given complex from Mycobacterium tuberculosis. Here we report the crystal structure and activity of a member of the VapBC family of complexes from M ...

    In prokaryotes, cognate toxin-antitoxin pairs have long been known, but no three-dimensional structure has been available for any given complex from Mycobacterium tuberculosis. Here we report the crystal structure and activity of a member of the VapBC family of complexes from M. tuberculosis. The toxin VapC-5 is a compact, 150 residues, two domain alpha/beta protein. Bent around the toxin is the VapB-5 antitoxin, a 33-residue alpha-helix. Assays suggest that the toxin is an Mg-enabled endoribonuclease, inhibited by the antitoxin. The lack of DNase activity is consistent with earlier suggestions that the complex represses its own operon. Furthermore, analysis of the interactions in the binding of the antitoxin to the toxin suggest that exquisite control is required to protect the bacteria cell from toxic VapC-5.


    Organizational Affiliation

    UCLA-DOE Institute of Genomics and Proteomics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1570, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA93Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0626MT0654vapB5
UniProt
Find proteins for P9WF19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WF19 
Go to UniProtKB:  P9WF19
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinB150Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv0627vapC5
EC: 3.1
UniProt
Find proteins for P96917 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P96917 
Go to UniProtKB:  P96917
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME

Download Ideal Coordinates CCD File 
H [auth B]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth B], D [auth B], E [auth B], F [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.83α = 90
b = 64.83β = 90
c = 164.65γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance