2DJH

Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5

Summary for 2DJH

• Entry DOI: 10.2210/pdb2djh/pdb
• Related: 2DFX
• Descriptor: Colicin-E5, 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE, 2'-DEOXYURIDINE 3'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: alpha/beta protein, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 13378.41

Authors

Yajima, S.,Inoue, S.,Ogawa, T.,Nonaka, T.,Ohsawa, K.,Masaki, H. (deposition date: 2006-04-03, release date: 2007-01-23, Last modification date: 2023-10-25)

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

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: 17099236
DOI: 10.1093/nar/gkl729

Experimental method

X-RAY DIFFRACTION (1.9 Å)