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Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator.

Charenton C, Taverniti V, Gaudon-Plesse C, Back R, Séraphin B, Graille M
Nat Struct Mol Biol 23 982-986 (2016)
Cited: 31 times
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Abstract

Elimination of the 5' cap of eukaryotic mRNAs, known as decapping, is considered to be a crucial, irreversible and highly regulated step required for the rapid degradation of mRNA by Xrn1, the major cytoplasmic 5'-3' exonuclease. Decapping is accomplished by the recruitment of a protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor. However, this complex has a low intrinsic enzymatic activity and requires several accessory proteins such as the Lsm1-7 complex, Pat1, Edc1-Edc2 and/or Edc3 to be fully active. Here we present the crystal structure of the active form of the yeast Kluyveromyces lactis Dcp1-Dcp2 enzyme bound to its product (m7GDP) and its potent activator Edc3. This structure of the Dcp1-Dcp2 complex bound to a cap analog further explains previously published data on substrate binding and provides hints as to the mechanism of Edc3-mediated Dcp2 activation.

Articles - 5lop mentioned but not cited (2)

  1. Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Wurm JP, Holdermann I, Overbeck JH, Mayer PHO, Sprangers R. Proc Natl Acad Sci U S A 114 6034-6039 (2017)
  2. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD. Nat Commun 9 1152 (2018)


Reviews citing this publication (11)

  1. Structural and molecular mechanisms for the control of eukaryotic 5'-3' mRNA decay. Mugridge JS, Coller J, Gross JD. Nat Struct Mol Biol 25 1077-1085 (2018)
  2. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Heck AM, Wilusz J. Cold Spring Harb Perspect Biol 10 a032839 (2018)
  3. The Regulatory Properties of the Ccr4-Not Complex. Chalabi Hagkarim N, Grand RJ. Cells 9 E2379 (2020)
  4. mRNA decapping: finding the right structures. Charenton C, Graille M. Philos Trans R Soc Lond B Biol Sci 373 20180164 (2018)
  5. Mille viae in eukaryotic mRNA decapping. Valkov E, Jonas S, Weichenrieder O. Curr Opin Struct Biol 47 40-51 (2017)
  6. Dcp2: an mRNA decapping enzyme that adopts many different shapes and forms. Wurm JP, Sprangers R. Curr Opin Struct Biol 59 115-123 (2019)
  7. Eukaryotic mRNA Decapping Activation. Vidya E, Duchaine TF. Front Genet 13 832547 (2022)
  8. Mutations in genes encoding regulators of mRNA decapping and translation initiation: links to intellectual disability. Weil D, Piton A, Lessel D, Standart N. Biochem Soc Trans 48 1199-1211 (2020)
  9. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. He F, Jacobson A. FEBS J 290 5057-5085 (2023)
  10. Structure and function of molecular machines involved in deadenylation-dependent 5'-3' mRNA degradation. Zhao Q, Pavanello L, Bartlam M, Winkler GS. Front Genet 14 1233842 (2023)
  11. Viral-Mediated mRNA Degradation for Pathogenesis. Du S, Liu X, Cai Q. Biomedicines 6 E111 (2018)

Articles citing this publication (18)

  1. A quantitative inventory of yeast P body proteins reveals principles of composition and specificity. Xing W, Muhlrad D, Parker R, Rosen MK. Elife 9 e56525 (2020)
  2. General decapping activators target different subsets of inefficiently translated mRNAs. He F, Celik A, Wu C, Jacobson A. Elife 7 e34409 (2018)
  3. A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast. Charenton C, Gaudon-Plesse C, Fourati Z, Taverniti V, Back R, Kolesnikova O, Séraphin B, Graille M. Proc Natl Acad Sci U S A 114 E9493-E9501 (2017)
  4. Control of mRNA decapping by autoinhibition. Paquette DR, Tibble RW, Daifuku TS, Gross JD. Nucleic Acids Res 46 6318-6329 (2018)
  5. Photocaged 5' cap analogues for optical control of mRNA translation in cells. Klöcker N, Weissenboeck FP, van Dülmen M, Špaček P, Hüwel S, Rentmeister A. Nat Chem 14 905-913 (2022)
  6. Quantitative reconstitution of yeast RNA processing bodies. Currie SL, Xing W, Muhlrad D, Decker CJ, Parker R, Rosen MK. Proc Natl Acad Sci U S A 120 e2214064120 (2023)
  7. DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli. Wang Q, Zhang D, Guan Z, Li D, Pei K, Liu J, Zou T, Yin P. Nucleic Acids Res 46 6880-6892 (2018)
  8. Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes. He F, Wu C, Jacobson A. Elife 11 e74410 (2022)
  9. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Cell Chem Biol 28 463-474.e7 (2021)
  10. An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome. Liu C, Mentzelopoulou A, Muhammad A, Volkov A, Weijers D, Gutierrez-Beltran E, Moschou PN. EMBO J 42 e111885 (2023)
  11. mRNAs biotinylated within the 5' cap and protected against decapping: new tools to capture RNA-protein complexes. Bednarek S, Madan V, Sikorski PJ, Bartenschlager R, Kowalska J, Jemielity J. Philos Trans R Soc Lond B Biol Sci 373 20180167 (2018)
  12. Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. Scheller U, Pfisterer K, Uebe S, Ekici AB, Reis A, Reis A, Jamra R, Ferrazzi F. BMC Med Genomics 11 41 (2018)
  13. mRNA decapping in 3D. Coller J. Nat Struct Mol Biol 23 954-956 (2016)
  14. Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis. Peters JK, Tibble RW, Warminski M, Jemielity J, Gross JD. Structure 30 721-732.e4 (2022)
  15. Structural Insight into Molecular Inhibitory Mechanism of InsP6 on African Swine Fever Virus mRNA-Decapping Enzyme g5Rp. Yang Y, Zhang C, Li X, Li L, Chen Y, Yang X, Zhao Y, Chen C, Wang W, Zhong Z, Yang C, Huang Z, Su D. J Virol 96 e0190521 (2022)
  16. Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs in Trypanosoma brucei. Schumacher MA, Henderson M, Zeng W. RNA 26 69-82 (2020)
  17. Pby1 is a direct partner of the Dcp2 decapping enzyme. Charenton C, Gaudon-Plesse C, Back R, Ulryck N, Cosson L, Séraphin B, Graille M. Nucleic Acids Res 48 6353-6366 (2020)
  18. LINE-1 mRNA 3' end dynamics shape its biology and retrotransposition potential. Janecki DM, Sen R, Szóstak N, Kajdasz A, Kordyś M, Plawgo K, Pandakov D, Philips A, Warkocki Z. Nucleic Acids Res 52 3327-3345 (2024)


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