2A6Q

Crystal structure of YefM-YoeB complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin

Kamada, K., Hanaoka, F.

(2005) Mol Cell 19: 497-509

  • DOI: 10.1016/j.molcel.2005.07.004
  • Primary Citation of Related Structures:  
    2A6Q, 2A6R, 2A6S

  • PubMed Abstract: 

    • The eubacterial chromosome encodes various addiction modules that control global levels of translation through RNA degradation. Crystal structures of the Escherichia coli YefM2 (antitoxin)-YoeB (toxin) complex and the free YoeB toxin have been determined ...

    The eubacterial chromosome encodes various addiction modules that control global levels of translation through RNA degradation. Crystal structures of the Escherichia coli YefM2 (antitoxin)-YoeB (toxin) complex and the free YoeB toxin have been determined. The structure of the heterotrimeric complex reveals an asymmetric disorder-to-order recognition strategy, in which one C terminus of the YefM homodimer exclusively interacts with an atypical microbial ribonuclease (RNase) fold of YoeB. Comparison with the YefM-free YoeB structure indicates a conformational rearrangement of the RNase catalytic site of YoeB, induced by interaction with YefM. Complementary biochemical experiments demonstrate that the YoeB toxin has an in vitro RNase activity that preferentially cleaves at the 3' end of purine ribonucleotides.

    Organizational Affiliation: 

    Cellular Physiology Laboratory, RIKEN Discovery Research Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. kamadak@riken.jp



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antitoxin yefMA, B, C, D86Escherichia coliMutation(s): 0 
Gene Names: yefM
UniProt
Find proteins for P69346 (Escherichia coli (strain K12))
Explore P69346 
Go to UniProtKB:  P69346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69346
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Toxin yoeBE, F84Escherichia coliMutation(s): 0 
Gene Names: yoeB
EC: 3.1
UniProt
Find proteins for P69348 (Escherichia coli (strain K12))
Explore P69348 
Go to UniProtKB:  P69348
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69348
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.485α = 90
b = 88.485β = 90
c = 135.15γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description