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Nucleic Acids Research Advance Access originally published online on November 11, 2006
Nucleic Acids Research 2006 34(21):6074-6082; doi:10.1093/nar/gkl729
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Nucleic Acids Research, 2006, Vol. 34, No. 21 6074-6082
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA–tRNA interaction

Shunsuke Yajima*, Sakura Inoue1, Tetsuhiro Ogawa1, Takamasa Nonaka2, Kanju Ohsawa and Haruhiko Masaki1,*

Department of Bioscience, Tokyo University of Agriculture Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan 1 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan 2 Department of Bioengineering, Nagaoka University of Technology Nagaoka, Niigata 940-2188, Japan

*To whom correspondence should be addressed. Tel: +81 3 5477 2768; Fax: +81 3 5477 2668; Email: yshun{at}nodai.ac.jp

Received May 15, 2006. Revised September 2, 2006. Accepted September 15, 2006.

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 Å. 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.

*Correspondence may also be addressed to Haruhiko Masaki. Tel: +81 3 5841 8248; Fax: +81 3 5841 8248; Email: hmasaki{at}mcb.bt.a.u-tokyo.ac.jp


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