4ngb › Citations

A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer.

Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ
Mol Cell 53 606-16 (2014)
Related entries: 4ngc, 4ngd, 4ngf, 4ngg, 4nh3, 4nh5, 4nh6, 4nha

Cited: 77 times
EuropePMC logo PMID: 24486018

Abstract

We have solved two families of crystal structures of the human Dicer "platform-PAZ-connector helix" cassette in complex with small interfering RNAs (siRNAs). The structures possess two adjacently positioned pockets: a 2 nt 3'-overhang-binding pocket within the PAZ domain (3' pocket) and a phosphate-binding pocket within the platform domain (phosphate pocket). One family of complexes contains a knob-like α-helical protrusion, designated "hDicer-specific helix," that separates the two pockets and orients the bound siRNA away from the surface of Dicer, which could be indicative of a product release/transfer state. In the second complex, the helical protrusion is melted/disordered and the bound siRNA is aligned toward the surface of Dicer, suggestive of a cleavage-competent state. These structures allow us to propose that the transition from the cleavage-competent to the postulated product release/transfer state may involve release of the 5'-phosphate from the phosphate pocket while retaining the 3' overhang in the 3' pocket.

Reviews - 4ngb mentioned but not cited (1)

  1. A Structural View of miRNA Biogenesis and Function. Leitão AL, Enguita FJ. Noncoding RNA 8 10 (2022)

Articles - 4ngb mentioned but not cited (3)

  1. A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ. Mol Cell 53 606-616 (2014)
  2. Increased Affinity for RNA Targets Evolved Early in Animal and Plant Dicer Lineages through Different Structural Mechanisms. Jia H, Kolaczkowski O, Rolland J, Kolaczkowski B. Mol Biol Evol 34 3047-3063 (2017)
  3. XGBPRH: Prediction of Binding Hot Spots at Protein⁻RNA Interfaces Utilizing Extreme Gradient Boosting. Deng L, Sui Y, Zhang J. Genes (Basel) 10 E242 (2019)


Reviews citing this publication (25)

  1. Regulation of microRNA biogenesis. Ha M, Kim VN. Nat Rev Mol Cell Biol 15 509-524 (2014)
  2. Regulation of microRNA function in animals. Gebert LFR, MacRae IJ. Nat Rev Mol Cell Biol 20 21-37 (2019)
  3. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Treiber T, Treiber N, Meister G. Nat Rev Mol Cell Biol 20 5-20 (2019)
  4. DICER1: mutations, microRNAs and mechanisms. Foulkes WD, Priest JR, Duchaine TF. Nat Rev Cancer 14 662-672 (2014)
  5. Double-Stranded RNA Sensors and Modulators in Innate Immunity. Hur S. Annu Rev Immunol 37 349-375 (2019)
  6. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Ipsaro JJ, Joshua-Tor L. Nat Struct Mol Biol 22 20-28 (2015)
  7. Molecular mechanisms of Dicer: endonuclease and enzymatic activity. Song MS, Rossi JJ. Biochem J 474 1603-1618 (2017)
  8. Mosquito Innate Immunity. Kumar A, Srivastava P, Sirisena P, Dubey SK, Kumar R, Shrinet J, Sunil S. Insects 9 E95 (2018)
  9. The many faces of Dicer: the complexity of the mechanisms regulating Dicer gene expression and enzyme activities. Kurzynska-Kokorniak A, Koralewska N, Pokornowska M, Urbanowicz A, Tworak A, Mickiewicz A, Figlerowicz M. Nucleic Acids Res 43 4365-4380 (2015)
  10. RNA Binding Proteins in the miRNA Pathway. Connerty P, Ahadi A, Hutvagner G. Int J Mol Sci 17 E31 (2015)
  11. RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors. Muhammad T, Zhang F, Zhang Y, Liang Y. Cells 8 E38 (2019)
  12. Trinucleotide expansion in disease: why is there a length threshold? Lee DY, McMurray CT. Curr Opin Genet Dev 26 131-140 (2014)
  13. Production of small RNAs by mammalian Dicer. Svobodova E, Kubikova J, Svoboda P. Pflugers Arch 468 1089-1102 (2016)
  14. A prokaryotic twist on argonaute function. Willkomm S, Zander A, Gust A, Grohmann D. Life (Basel) 5 538-553 (2015)
  15. Sensing viral RNAs by Dicer/RIG-I like ATPases across species. Paro S, Imler JL, Meignin C. Curr Opin Immunol 32 106-113 (2015)
  16. Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway. Shelton SB, Reinsborough C, Xhemalce B. PLoS Genet 12 e1006139 (2016)
  17. A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective. Paturi S, Deshmukh MV. Front Mol Biosci 8 643657 (2021)
  18. Insecticidal RNA interference, thinking beyond long dsRNA. Flynt AS. Pest Manag Sci 77 2179-2187 (2021)
  19. Modulation of MicroRNA Processing by Dicer via Its Associated dsRNA Binding Proteins. Yoshida T, Asano Y, Ui-Tei K. Noncoding RNA 7 57 (2021)
  20. DICER: structure, function, and regulation. Vergani-Junior CA, Tonon-da-Silva G, Inan MD, Mori MA. Biophys Rev 13 1081-1090 (2021)
  21. Untangling the roles of RNA helicases in antiviral innate immunity. Baldaccini M, Pfeffer S. PLoS Pathog 17 e1010072 (2021)
  22. Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases. Ciechanowska K, Pokornowska M, Kurzyńska-Kokorniak A. Int J Mol Sci 22 E616 (2021)
  23. Dicer structure and function: conserved and evolving features. Zapletal D, Kubicek K, Svoboda P, Stefl R. EMBO Rep 24 e57215 (2023)
  24. RNase III, Ribosome Biogenesis and Beyond. Lejars M, Kobayashi A, Hajnsdorf E. Microorganisms 9 2608 (2021)
  25. miRNA in head and neck squamous cell carcinomas: promising but still distant future of personalized oncology. Kozłowska-Masłoń J, Guglas K, Kolenda T, Lamperska K, Makałowska I. Rep Pract Oncol Radiother 28 681-697 (2023)

Articles citing this publication (48)

  1. Functional Anatomy of the Human Microprocessor. Nguyen TA, Jo MH, Choi YG, Park J, Kwon SC, Hohng S, Kim VN, Woo JS. Cell 161 1374-1387 (2015)
  2. Structure of Human DROSHA. Kwon SC, Nguyen TA, Choi YG, Jo MH, Hohng S, Kim VN, Woo JS. Cell 164 81-90 (2016)
  3. A variety of dicer substrates in human and C. elegans. Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N. Cell 159 1153-1167 (2014)
  4. Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage. Burger K, Schlackow M, Potts M, Hester S, Mohammed S, Gullerova M. J Cell Biol 216 2373-2389 (2017)
  5. Resistance to cancer chemotherapeutic drugs is determined by pivotal microRNA regulators. Geretto M, Pulliero A, Rosano C, Zhabayeva D, Bersimbaev R, Izzotti A. Am J Cancer Res 7 1350-1371 (2017)
  6. Dicer uses distinct modules for recognizing dsRNA termini. Sinha NK, Iwasa J, Shen PS, Bass BL. Science 359 329-334 (2018)
  7. SRSF3 recruits DROSHA to the basal junction of primary microRNAs. Kim K, Nguyen TD, Li S, Nguyen TA. RNA 24 892-898 (2018)
  8. TRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments. Fareh M, Yeom KH, Haagsma AC, Chauhan S, Heo I, Joo C. Nat Commun 7 13694 (2016)
  9. Long Noncoding RNA MPRL Promotes Mitochondrial Fission and Cisplatin Chemosensitivity via Disruption of Pre-miRNA Processing. Tian T, Lv X, Pan G, Lu Y, Chen W, He W, Lei X, Zhang H, Liu M, Sun S, Ou Z, Lin X, Cai L, He L, Tu Z, Wang X, Tannous BA, Ferrone S, Li J, Fan S. Clin Cancer Res 25 3673-3688 (2019)
  10. Drosophila dicer-2 cleavage is mediated by helicase- and dsRNA termini-dependent states that are modulated by Loquacious-PD. Sinha NK, Trettin KD, Aruscavage PJ, Bass BL. Mol Cell 58 406-417 (2015)
  11. Heme enables proper positioning of Drosha and DGCR8 on primary microRNAs. Partin AC, Ngo TD, Herrell E, Jeong BC, Hon G, Nam Y. Nat Commun 8 1737 (2017)
  12. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Kandasamy SK, Fukunaga R. Proc Natl Acad Sci U S A 113 14031-14036 (2016)
  13. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S, Jacobsen SE, Du J. Science 374 1152-1157 (2021)
  14. Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites. Sheng P, Fields C, Aadland K, Wei T, Kolaczkowski O, Gu T, Kolaczkowski B, Xie M. Nucleic Acids Res 46 5737-5752 (2018)
  15. Microprocessor depends on hemin to recognize the apical loop of primary microRNA. Nguyen TA, Park J, Dang TL, Choi YG, Kim VN. Nucleic Acids Res 46 5726-5736 (2018)
  16. Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains. Masliah G, Maris C, König SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FH. EMBO J 37 e97089 (2018)
  17. Structural basis of microRNA processing by Dicer-like 1. Wei X, Ke H, Wen A, Gao B, Shi J, Feng Y. Nat Plants 7 1389-1396 (2021)
  18. Revealing a new activity of the human Dicer DUF283 domain in vitro. Kurzynska-Kokorniak A, Pokornowska M, Koralewska N, Hoffmann W, Bienkowska-Szewczyk K, Figlerowicz M. Sci Rep 6 23989 (2016)
  19. The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Pokornowska M, Milewski MC, Ciechanowska K, Szczepańska A, Wojnicka M, Radogostowicz Z, Figlerowicz M, Kurzynska-Kokorniak A. Cell Mol Life Sci 77 3231-3244 (2020)
  20. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O'Carroll D, Stefl R, Svoboda P. Mol Cell 82 4064-4079.e13 (2022)
  21. Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Jouravleva K, Golovenko D, Demo G, Dutcher RC, Hall TMT, Zamore PD, Korostelev AA. Mol Cell 82 4049-4063.e6 (2022)
  22. Secondary structure RNA elements control the cleavage activity of DICER. Nguyen TD, Trinh TA, Bao S, Nguyen TA. Nat Commun 13 2138 (2022)
  23. Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex. Yamaguchi S, Naganuma M, Nishizawa T, Kusakizako T, Tomari Y, Nishimasu H, Nureki O. Nature 607 393-398 (2022)
  24. A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation. Loffer A, Singh J, Fukudome A, Mishra V, Wang F, Pikaard CS. Elife 11 e73260 (2022)
  25. Dissecting protein domain variability in the core RNA interference machinery of five insect orders. Arraes FBM, Martins-de-Sa D, Noriega Vasquez DD, Melo BP, Faheem M, de Macedo LLP, Morgante CV, Barbosa JARG, Togawa RC, Moreira VJV, Danchin EGJ, Grossi-de-Sa MF. RNA Biol 18 1653-1681 (2021)
  26. Loquacious-PD removes phosphate inhibition of Dicer-2 processing of hairpin RNAs into siRNAs. Fukunaga R. Biochem Biophys Res Commun 498 1022-1027 (2018)
  27. Short Hairpin RNAs for Strand-Specific Small Interfering RNA Production. Sheng P, Flood KA, Xie M. Front Bioeng Biotechnol 8 940 (2020)
  28. Modeling of the catalytic core of Arabidopsis thaliana Dicer-like 4 protein and its complex with double-stranded RNA. Mickiewicz A, Sarzyńska J, Miłostan M, Kurzyńska-Kokorniak A, Rybarczyk A, Łukasiak P, Kuliński T, Figlerowicz M, Błażewicz J. Comput Biol Chem 66 44-56 (2017)
  29. Overexpression and purification of Dicer and accessory proteins for biochemical and structural studies. Sinha NK, Bass BL. Methods 126 54-65 (2017)
  30. RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity. Koralewska N, Szczepanska A, Ciechanowska K, Wojnicka M, Pokornowska M, Milewski MC, Gudanis D, Baranowski D, Nithin C, Bujnicki JM, Gdaniec Z, Figlerowicz M, Kurzynska-Kokorniak A. Cell Mol Life Sci 78 3709-3724 (2021)
  31. Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self-nonself discrimination. Singh RK, Jonely M, Leslie E, Rejali NA, Noriega R, Bass BL. Elife 10 e65810 (2021)
  32. Unknown Areas of Activity of Human Ribonuclease Dicer: A Putative Deoxyribonuclease Activity. Wojnicka M, Szczepanska A, Kurzynska-Kokorniak A. Molecules 25 E1414 (2020)
  33. Characterization of DCL4 missense alleles provides insights into its ability to process distinct classes of dsRNA substrates. Montavon T, Kwon Y, Zimmermann A, Hammann P, Vincent T, Cognat V, Bergdoll M, Michel F, Dunoyer P. Plant J 95 204-218 (2018)
  34. Characterization of a naturally occurring truncated Dicer. Mosca N, Starega-Roslan J, Castiello F, Russo A, Krzyzosiak WJ, Potenza N. Mol Biol Rep 42 1333-1340 (2015)
  35. Sequence determinant of small RNA production by DICER. Lee YY, Kim H, Kim VN. Nature 615 323-330 (2023)
  36. Structure of the human DICER-pre-miRNA complex in a dicing state. Lee YY, Lee H, Kim H, Kim VN, Roh SH. Nature 615 331-338 (2023)
  37. A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis. Fukunaga R, Zamore PD. Cell Cycle 13 1671-1676 (2014)
  38. Sequence- and structure-based analysis of proteins involved in miRNA biogenesis. Sharma C, Mohanty D. J Biomol Struct Dyn 36 139-151 (2018)
  39. Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions. Jiang Y, Liu HF, Liu R. PLoS Comput Biol 17 e1008951 (2021)
  40. Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain. Chen S, Liu W, Naganuma M, Tomari Y, Iwakawa HO. Nucleic Acids Res 50 4669-4684 (2022)
  41. TRBP-Dicer interaction may enhance HIV-1 TAR RNA translation via TAR RNA processing, repressing host-cell apoptosis. Komori C, Takahashi T, Nakano Y, Ui-Tei K. Biol Open 9 bio050435 (2020)
  42. The Significance of the DUF283 Domain for the Activity of Human Ribonuclease Dicer. Szczepanska A, Wojnicka M, Kurzynska-Kokorniak A. Int J Mol Sci 22 8690 (2021)
  43. Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL. Elife 12 e85120 (2023)
  44. High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension. Bouvette J, Korkut DN, Fouillen A, Amellah S, Nanci A, Durocher Y, Omichinski JG, Legault P. BMC Biotechnol 18 76 (2018)
  45. Posttranscriptional Regulation of the Human ABCG2 Multidrug Transporter Protein by Artificial Mirtrons. Schamberger A, Várady G, Fóthi Á, Orbán TI. Genes (Basel) 12 1068 (2021)
  46. The Effect of Dicer Knockout on RNA Interference Using Various Dicer Substrate Small Interfering RNA (DsiRNA) Structures. Song MS, Alluin J, Rossi JJ. Genes (Basel) 13 436 (2022)
  47. DICER1 platform domain missense variants inhibit miRNA biogenesis and lead to tumor susceptibility. Pelletier D, Chong AL, Wu M, Witkowski L, Albert S, Sabbaghian N, Fabian MR, Foulkes WD. NAR Cancer 5 zcad030 (2023)
  48. Single nucleotide polymorphisms in microRNAs action as biomarkers for breast cancer. Nguyen TTN, Tran MTH, Nguyen VTL, Nguyen UDP, Nguyen GDT, Huynh LH, Nguyen HT. Turk J Biol 44 284-294 (2020)


Quick links