3BPQ

Crystal Structure of RelB-RelE antitoxin-toxin complex from Methanococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of the antitoxin-toxin protein complex RelB-RelE from Methanococcus jannaschii

Francuski, D.Saenger, W.

(2009) J Mol Biol 393: 898-908

  • DOI: 10.1016/j.jmb.2009.08.048
  • Primary Citation of Related Structures:  
    3BPQ

  • PubMed Abstract: 
  • Here we present the crystal structure of the Methanococcus jannaschii RelE-RelB (RelBE) toxin-antitoxin (TA) protein complex determined by the MIRAS (multiple isomorphous replacement with anomalous signal) method. The genes encoding this TA system are located in the chromosome of this archaeon and involved in stress response ...

    Here we present the crystal structure of the Methanococcus jannaschii RelE-RelB (RelBE) toxin-antitoxin (TA) protein complex determined by the MIRAS (multiple isomorphous replacement with anomalous signal) method. The genes encoding this TA system are located in the chromosome of this archaeon and involved in stress response. RelE acts as an endoribonuclease that cleaves mRNA on the ribosome, and we compare the RelBE complex to the known structures of other TA systems belonging to this group and to endoribonucleases. M. jannaschii RelBE forms a heterotetramer with the antitoxin in the centre of the complex, a configuration that differs vastly from the heterotetramer structure of the previously published RelBE from another archaeon, Pyrococcus horikoshii. The long N-terminal alpha-helix of the tightly bound M. jannaschii antitoxin RelB covers the presumed active site of the toxin RelE that is formed by a central beta-sheet, a loop on one side and a C-terminal alpha-helix on the other side. The active site of the M. jannaschii toxin RelE harbours positive charges that are thought to neutralize the negative charges of the substrate mRNA, including Arg62 that was changed to Ser62 by the Escherichia coli expression system, thereby leading to inactive toxin RelE. Comparative studies suggest that Asp43 and His79 are also involved in the activity of the toxin.


    Organizational Affiliation

    Kristallographie, Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 6, Berlin 14195, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin RelB3A, C52Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: relB3relBMJ1103.1
UniProt
Find proteins for P0CL56 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P0CL56 
Go to UniProtKB:  P0CL56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL56
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toxin RelE3B, D88Methanocaldococcus jannaschii DSM 2661Mutation(s): 1 
Gene Names: MJ1103relErelE3
EC: 3.1
UniProt
Find proteins for Q58503 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58503 
Go to UniProtKB:  Q58503
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58503
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.794α = 90
b = 57.992β = 92.3
c = 58.747γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2011-08-31
    Changes: Database references, Structure summary
  • Version 1.4: 2017-10-25
    Changes: Refinement description