2DFX
Crystal structure of the carboxy terminal domain of colicin E5 complexed with its inhibitor
Summary for 2DFX
| Entry DOI | 10.2210/pdb2dfx/pdb |
| Related | 2DJH |
| Descriptor | Colicin-E5, Colicin-E5 immunity protein (3 entities in total) |
| Functional Keywords | alpha/beta protein, protein-inhibitor protein complex, hydrolase |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 2 |
| Total formula weight | 24680.58 |
| Authors | Yajima, S.,Inoue, S.,Ogawa, T.,Nonaka, T.,Ohsawa, K.,Masaki, H. (deposition date: 2006-03-06, release date: 2007-01-23, Last modification date: 2025-04-30) |
| Primary citation | Yajima, S.,Inoue, S.,Ogawa, T.,Nonaka, T.,Ohsawa, K.,Masaki, H. Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction Nucleic Acids Res., 34:6074-6082, 2006 Cited by PubMed Abstract: 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. PubMed: 17099236DOI: 10.1093/nar/gkl729 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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