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Nucleic Acids Research Advance Access published online on July 19, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn458
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© 2008 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

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition

Takashi Nagata1, Sakura Suzuki1, Ryuta Endo1, Mikako Shirouzu1, Takaho Terada1, Makoto Inoue1, Takanori Kigawa1,2, Naohiro Kobayashi1, Peter Güntert1, Akiko Tanaka1, Yoshihide Hayashizaki1, Yutaka Muto1 and Shigeyuki Yokoyama1,3,*

1Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, 2Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502 and 3Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

*To whom correspondence should be addressed. Tel: +81 45 50 39 196; Fax: +81 45 50 39 201; Email: yokoyama{at}biochem.s.u-tokyo.ac.jp Correspondence may also be addressed to Yutaka Muto. Tel: +81 45 50 39 461; Fax: +81 45 50 39 460; Email: ymuto{at}gsc.riken.jp

Received April 11, 2008. Revised June 30, 2008. Accepted July 2, 2008.

The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3' specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m7GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m7GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic {alpha}-helical extension at its C-terminus, which covers the β-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N7-methyl guanosine (m7G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second β-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.

Present address: Takashi Nagata, Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

Peter Güntert, Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, J. W. Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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