Solution structure of the Drosha double-stranded RNA-binding domain

Silence

Volumn 1, Issue 1, 2010, Pages

  Mueller, Geoffrey A ^a   Miller, Matthew T ^a   DeRose, Eugene F ^a   Ghosh, Mahua ^a   London, Robert E ^a   Hall, Traci M T ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIGEORGE SYNDROME CRITICAL REGION 8 PROTEIN; DOUBLE STRANDED RNA; DROSHA PROTEIN; RIBONUCLEASE III; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BETA SHEET; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME BINDING; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN RNA BINDING; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 78650324516     PISSN: None     EISSN: 1758907X     Source Type: Journal    
DOI: 10.1186/1758-907X-1-2     Document Type: Article

References (37)

1. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002, 21:4663-4670. 10.1093/emboj/cdf476, 126204, 12198168.
2. Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009, 10:126-139. 10.1038/nrm2632, 19165215.
3. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419. 10.1038/nature01957, 14508493.
4. Bohnsack MT, Czaplinski K, Gorlich D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 2004, 10:185-191. 10.1261/rna.5167604, 1370530, 14730017.
5. Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science 2004, 303:95-98. 10.1126/science.1090599, 14631048.
6. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 2005, 102:3691-3696. 10.1073/pnas.0405570102, 553294, 15738428.
7. Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003, 17:3011-3016. 10.1101/gad.1158803, 305252, 14681208.
8. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001, 409:363-366. 10.1038/35053110, 11201747.
9. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 2001, 106:23-34. 10.1016/S0092-8674(01)00431-7, 11461699.
10. Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Science 2001, 293:834-838. 10.1126/science.1062961, 11452083.
11. Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 2001, 15:2654-2659. 10.1101/gad.927801, 312808, 11641272.
12. Knight SW, Bass BL. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 2001, 293:2269-2271. 10.1126/science.1062039, 1855227, 11486053.
13. Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 2002, 12:1484-1495. 10.1016/S0960-9822(02)01017-5, 12225663.
14. Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 2004, 18:3016-3027. 10.1101/gad.1262504, 535913, 15574589.
15. Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ. Processing of primary microRNAs by the microprocessor complex. Nature 2004, 432:231-235. 10.1038/nature03049, 15531879.
16. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R. The microprocessor complex mediates the genesis of microRNAs. Nature 2004, 432:235-240. 10.1038/nature03120, 15531877.
17. Landthaler M, Yalcin A, Tuschl T. The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 2004, 14:2162-2167. 10.1016/j.cub.2004.11.001, 15589161.
18. Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006, 125:887-901. 10.1016/j.cell.2006.03.043, 16751099.
19. Sohn SY, Bae WJ, Kim JJ, Yeom KH, Kim VN, Cho Y. Crystal structure of human DGCR8 core. Nat Struct Mol Biol 2007, 14:847-853. 10.1038/nsmb1294, 17704815.
20. Yeom KH, Lee Y, Han J, Suh MR, Kim VN. Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res 2006, 34:4622-4629. 10.1093/nar/gkl458, 1636349, 16963499.
21. Zeng Y, Cullen BR. Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J Biol Chem 2005, 280:27595-27603. 10.1074/jbc.M504714200, 15932881.
22. Tian B, Bevilacqua PC, Diegelman-Parente A, Mathews MB. The double-stranded-RNA-binding motif: interference and much more. Nat Rev Mol Cell Biol 2004, 5:1013-1023. 10.1038/nrm1528, 15573138.
23. Wu H, Henras A, Chanfreau G, Feigon J. Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III. Proc Natl Acad Sci USA 2004, 101:8307-8312. 10.1073/pnas.0402627101, 420390, 15150409.
24. Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 2006, 124:355-366. 10.1016/j.cell.2005.11.034, 16439209.
25. Ramos A, Bayer P, Varani G. Determination of the structure of the RNA complex of a double-stranded RNA-binding domain from Drosophila Staufen protein. Biopolymers 1999, 52:181-196. 10.1002/1097-0282(1999)52:4<181::AID-BIP1003>3.0.CO;2-5, 11295750.
26. Ryter JM, Schultz SC. Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. EMBO J 1998, 17:7505-7513. 10.1093/emboj/17.24.7505, 1171094, 9857205.
27. Lahm A, Suck D. DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. J Mol Biol 1991, 222:645-667. 10.1016/0022-2836(91)90502-W, 1748997.
28. Ledvina PS, Yao N, Choudhary A, Quiocho FA. Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc Natl Acad Sci USA 1996, 93:6786-6791. 10.1073/pnas.93.13.6786, 39105, 8692896.
29. Zeng Y, Yi R, Cullen BR. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J 2005, 24:138-148. 10.1038/sj.emboj.7600491, 544904, 15565168.
30. Mueller GA, Moon AF, Derose EF, Havener JM, Ramsden DA, Pedersen LC, London RE. A comparison of BRCT domains involved in nonhomologous end-joining: introducing the solution structure of the BRCT domain of polymerase lambda. DNA Repair (Amst) 2008, 7:1340-1351. 10.1016/j.dnarep.2008.04.018, 2583787, 18585102.
31. Herrmann T, Guntert P, Wuthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 2002, 319:209-227. 10.1016/S0022-2836(02)00241-3, 12051947.
32. Xu Y, Long D, Yang D. Rapid data collection for protein structure determination by NMR spectroscopy. J Am Chem Soc 2007, 129:7722-7723. 10.1021/ja071442e, 17536800.
33. Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM. The Xplor-NIH NMR molecular structure determination package. J Magn Reson 2003, 160:65-73. 10.1016/S1090-7807(02)00014-9, 12565051.
34. Grishaev A, Bax A. An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation. J Am Chem Soc 2004, 126:7281-7292. 10.1021/ja0319994, 15186165.
35. Leulliot N, Quevillon-Cheruel S, Graille M, van Tilbeurgh H, Leeper TC, Godin KS, Edwards TE, Sigurdsson ST, Rozenkrants N, Nagel RJ, Ares M, Varani G. A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III. EMBO J 2004, 23:2468-2477. 10.1038/sj.emboj.7600260, 449770, 15192703.
36. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001, 98:10037-10041. 10.1073/pnas.181342398, 56910, 11517324.
37. DeLano WL. The PyMOL molecular graphics system. 2002, San Carlos, CA, USA: DeLano Scientific.