title: The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
abstract: 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 m(7)GpppG 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 m(7)GpppG 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 beta-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N(7)-methyl guanosine (m(7)G) 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 beta-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.
authors.affiliation: Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagata
authors.forename: Sakura
authors.initials: S
authors.lastname: Suzuki
authors.forename: Ryuta
authors.initials: R
authors.lastname: Endo
authors.forename: Mikako
authors.initials: M
authors.lastname: Shirouzu
authors.forename: Takaho
authors.initials: T
authors.lastname: Terada
authors.forename: Makoto
authors.initials: M
authors.lastname: Inoue
authors.forename: Takanori
authors.initials: T
authors.lastname: Kigawa
authors.forename: Naohiro
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Peter
authors.initials: P
authors.lastname: Güntert
authors.forename: Akiko
authors.initials: A
authors.lastname: Tanaka
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Muto
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D015226:Dinucleoside Phosphates / Q000737:chemistry* / Q000378:metabolism; D005095:Exoribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012314:RNA Cap Analogs / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D015226:Dinucleoside Phosphates; D005095:Exoribonucleases; D012314:RNA Cap Analogs; C062229:7-methyl-diguanosine triphosphate