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

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Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Güntert P, Tanaka A, Hayashizaki Y, Muto Y, Yokoyama S
OpenAccess logo Nucleic Acids Res 36 4754-67 (2008)
Cited: 31 times
EuropePMC logo PMID: 18641416

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.

Articles - 2rok mentioned but not cited (1)

  1. The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition. Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Güntert P, Tanaka A, Hayashizaki Y, Muto Y, Yokoyama S. Nucleic Acids Res 36 4754-4767 (2008)


Reviews citing this publication (10)

  1. Cap and cap-binding proteins in the control of gene expression. Topisirovic I, Svitkin YV, Sonenberg N, Shatkin AJ. Wiley Interdiscip Rev RNA 2 277-298 (2011)
  2. RNA-modifying proteins as anticancer drug targets. Boriack-Sjodin PA, Ribich S, Copeland RA. Nat Rev Drug Discov 17 435-453 (2018)
  3. Poly(A)-specific ribonuclease (PARN): an allosterically regulated, processive and mRNA cap-interacting deadenylase. Virtanen A, Henriksson N, Nilsson P, Nissbeck M. Crit Rev Biochem Mol Biol 48 192-209 (2013)
  4. Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems. Muto Y, Yokoyama S. Wiley Interdiscip Rev RNA 3 229-246 (2012)
  5. Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. Arraiano CM, Mauxion F, Viegas SC, Matos RG, Séraphin B. Biochim Biophys Acta 1829 491-513 (2013)
  6. Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Godwin AR, Kojima S, Green CB, Wilusz J. Biochim Biophys Acta 1829 571-579 (2013)
  7. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. Borden KLB, Volpon L. RNA Biol 17 1239-1251 (2020)
  8. FXR1a-associated microRNP: A driver of specialized non-canonical translation in quiescent conditions. Bukhari SI, Vasudevan S. RNA Biol 14 137-145 (2017)
  9. NCBP3: A Multifaceted Adaptive Regulator of Gene Expression. Rambout X, Maquat LE. Trends Biochem Sci 46 87-96 (2021)
  10. The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation. Huynh TN, Parker R. J Biol Chem 299 105139 (2023)

Articles citing this publication (20)



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