2dfx
| |||||||||
| 2dfx, resolution 1.90Å () | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Related: | 2djh | ||||||||
| |||||||||
| |||||||||
| |||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor
OverviewOverview
Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.
About this StructureAbout this Structure
2DFX is a Protein complex structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction., Yajima S, Inoue S, Ogawa T, Nonaka T, Ohsawa K, Masaki H, Nucleic Acids Res. 2006;34(21):6074-82. Epub 2006 Nov 11. PMID:17099236 Page seeded by OCA on Sun May 4 00:20:33 2008