The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition
2008
Nagata, Takashi | Suzuki, Sakura | Endo, Ryuta | Shirouzu, Mikako | Terada, Takaho | Inoue, Makoto | Kigawa, Takanori | Kobayashi, Naohiro | Güntert, Peter | Tanaka, Akiko | Hayashizaki, Yoshihide | Muto, Yutaka | Yokoyama, Shigeyuki
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 α-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.
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