3DBO | pdb_00003dbo

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

PDB DOI: https://doi.org/10.2210/pdb3DBO/pdb

Classification: TOXIN/ANTITOXIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-02 Released: 2008-07-15
Deposition Author(s): Miallau, L., Cascio, D., Eisenberg, D., Integrated Center for Structure and Function Innovation (ISFI), TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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 Biological Chem 284: 276-283

PubMed: 18952600 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M805061200
Primary Citation 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. 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, the Department of Biological Chemistry, David Geffen School of Medicine, Molecular Cell and Developmental Biology, and the Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1570.

Macromolecule Content

Total Structure Weight: 26.65 kDa
Atom Count: 1,330
Modeled Residue Count: 160
Deposited Residue Count: 243
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	93	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv0626, MT0654
UniProt
Find proteins for P9WF19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WF19 Go to UniProtKB: P9WF19
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WF19
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B	150	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv0627 EC: 3.1
UniProt
Find proteins for P96917 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96917 Go to UniProtKB: P96917
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96917
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	C [auth B], D [auth B], E [auth B], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.213 (Depositor), 0.211 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.83	α = 90
b = 64.83	β = 90
c = 164.65	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-07-15

Deposition Author(s):

Miallau, L.

Cascio, D.

Eisenberg, D.

Integrated Center for Structure and Function Innovation (ISFI)

TB Structural Genomics Consortium (TBSGC)

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
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations