3OEI

Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes.

Miallau, L.Jain, P.Arbing, M.A.Cascio, D.Phan, T.Ahn, C.J.Chan, S.Chernishof, I.Maxson, M.Chiang, J.Jacobs Jr., W.R.Eisenberg, D.S.

(2013) Structure 21: 627-637

  • DOI: https://doi.org/10.1016/j.str.2013.02.008
  • Primary Citation of Related Structures:  
    3G5O, 3OEI

  • PubMed Abstract: 

    The Mycobacterium tuberculosis (Mtb) genome encodes approximately 90 toxin-antitoxin protein complexes, including three RelBE family members, which are believed to play a major role in bacterial fitness and pathogenicity. We have determined the crystal structures of Mtb RelBE-2 and RelBE-3, and the structures reveal homologous heterotetramers. Our structures suggest RelE-2, and by extension the closely related RelE-1, use a different catalytic mechanism than RelE-3, because our analysis of the RelE-2 structure predicts additional amino acid residues that are likely to be functionally significant and are missing from analogous positions in the RelE-3 structure. Toxicity assays corroborate our structural findings; overexpression of RelE-3, whose active site is more similar to Escherichia coli YoeB, has limited consequences on bacterial growth, whereas RelE-1 and RelE-2 overexpression results in acute toxicity. Moreover, RelE-2 overexpression results in an elongated cell phenotype in Mycobacterium smegmatis and protects M. tuberculosis against antibiotics, suggesting a different functional role for RelE-2.


  • Organizational Affiliation

    Howard Hughes Medical Institute and UCLA-DOE Institute for Genomics and Proteomics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095-1570, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RelJ (Antitoxin Rv3357)
A, B, I, J, M
A, B, I, J, M, N
98Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3357MT3465MTV004.14
UniProt
Find proteins for P9WF25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WF25 
Go to UniProtKB:  P9WF25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WF25
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RelK (Toxin Rv3358)
C, D, G, H, K
C, D, G, H, K, L, O, P
96Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3358MT3466MTV004.15
EC: 3.1
UniProt
Find proteins for P9WF09 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WF09 
Go to UniProtKB:  P9WF09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WF09
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RelJ (Antitoxin Rv3357)
E, F
98Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3357MT3465MTV004.14
UniProt
Find proteins for P9WF25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WF25 
Go to UniProtKB:  P9WF25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WF25
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
Q [auth C]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
E, F
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.219α = 90
b = 187.512β = 94.46
c = 113.881γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Adxvdata processing
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2022-11-23
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description