2A6Q image
Deposition Date 2005-07-04
Release Date 2005-08-23
Last Version Date 2024-03-13
Entry Detail
PDB ID:
2A6Q
Keywords:
TOXIN INHIBITOR/TOXIN
Title:
Crystal structure of YefM-YoeB complex
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.05 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 64
2A6Q validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antitoxin yefM
Gene (Uniprot):yefM
Chain IDs:A, B, C, D
Chain Length:86
Number of Molecules:4
Biological Source:Escherichia coli
UniProt ID:P69346 Pfam ID:PF02604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Toxin yoeB
Gene (Uniprot):yoeB
Chain IDs:E, F
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P69348 Pfam ID:PF06769
Primary Citation
Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin
Mol.Cell 19 497 509 (2005)
PMID: 16109374 DOI: 10.1016/j.molcel.2005.07.004

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
2A6R
2A6S