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 

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:  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 determ ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antitoxin yefM
A, B, C, D
86Escherichia coli (strain K12)Gene Names: yefM
Find proteins for P69346 (Escherichia coli (strain K12))
Go to UniProtKB:  P69346
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Toxin yoeB
E, F
84Escherichia coli (strain K12)Gene Names: yoeB
EC: 3.1.-.-
Find proteins for P69348 (Escherichia coli (strain K12))
Go to UniProtKB:  P69348
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 88.485α = 90.00
b = 88.485β = 90.00
c = 135.150γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
DMphasing
PDB_EXTRACTdata extraction
CCP4data scaling
MLPHAREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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