5lj5

Structural highlights

Function

[PRP19_YEAST] Involved in pre-mRNA splicing. Acts a central component of the NTC complex (or PRP19-associated complex) that associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Involved in DNA repair. [PRP16_YEAST] Influences the fidelity of branchpoint recognition in yeast splicing. This is RNA-dependent ATPase which is essential for viability. It may mediate one of the many ATP-requiring steps of spliceosome assembly and that accuracy of branchpoint recognition may be coupled to ATP binding and/or hydrolysis.^[1] [CLF1_YEAST] Involved in pre-mRNA splicing and cell cycle progression. Required for the spliceosome assembly by promoting the functional integration of the U4/U6.U5 tri-snRNP particle into the U1-, U2-dependent pre-spliceosome. Also recruits PRP19 to the spliceosome, as a component of the NTC complex (or PRP19-associated complex). The association of the NTC complex to the spliceosome mediates conformational rearrangement or stabilizes the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Required for initiation of the DNA replication by binding the RNA replication origins, probably through its interaction with the origin recognition complex (ORC).^{[2] [3] [4] [5] [6]} [BRR2_YEAST] RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. Involved in spliceosome assembly, activation and disassembly. Mediates changes in the dynamic network of RNA-RNA interactions in the spliceosome. Catalyzes the ATP-dependent unwinding of U4/U6 RNA duplices, an essential step in the assembly of a catalytically active spliceosome.^{[7] [8] [9] [10]} [RUXF_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [SLT11_YEAST] Involved in pre-mRNA splicing. Facilitates the cooperative formation of U2/U6 helix II in association with stem II in the spliceosome. Binds to RNA.^{[11] [12]} [CEF1_YEAST] Involved in pre-mRNA splicing and cell cycle control. Required for the binding of the NTC complex (or PRP19-associated complex) components to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. Its absence leads to an arrest of the cell cycle, possibly due to the inefficient splicing of TUB1.^{[13] [14] [15] [16]} [RU2A_YEAST] Involved in pre-mRNA splicing. Associates to U2 snRNA in a MSL1 dependent manner and is required for normal accumulation of U2 snRNA. Required for the spliceosome assembly and the efficient addition of U2 snRNP onto the pre-mRNA.^[17] [CWC2_YEAST] Involved in the first step of pre-mRNA splicing. Required for cell growth and cell cycle control. Plays a role in the levels of the U1, U4, U5 and U6 snRNAs and the maintenance of the U4/U6 snRNA complex. May provide the link between the "nineteen complex" NTC spliceosome protein complex and the spliceosome through the U6 snRNA. Associates predominantly with U6 snRNAs in assembled active spliceosomes. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Binds also to U1, U4, U5 and U6 snRNAs and to pre-mRNAs, in vitro. Is not required for the Prp2-mediated remodeling of the activated spliceosome.^{[18] [19]} [RUXG_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [RUXE_YEAST] Involved in pre-mRNA splicing. Binds and is required for the stability of snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Involved in cap modification.^[20] [SMD1_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.^{[21] [22]} [CWC21_YEAST] Involved in pre-mRNA splicing. May function at or prior to the first catalytic step of splicing at the catalytic center of the spliceosome, together with ISY1. May do so by stabilizing the catalytic center or the position of the RNA substrate.^{[23] [24]} [PRP45_YEAST] Involved in pre-mRNA splicing. Associated with the spliceosome throughout the splicing reactions, until after the second catalytic step.^{[25] [26]} [SMD3_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.^{[27] [28]} [SN114_YEAST] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [MSL1_YEAST] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA.^[29] [ISY1_YEAST] Involved in pre-mRNA splicing and cell cycle control. As a component of the NTC complex (or PRP19-associated complex), associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation. The cell cycle arrest of SYF2 defective cells may be due to the inefficient splicing of TUB1. Also involved in DNA repair.^{[30] [31] [32]} [SYF1_YEAST] Involved in pre-mRNA splicing and cell cycle control. As a component of the NTC complex (or PRP19-associated complex), associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation.^{[33] [34]} [PRP46_YEAST] Involved in pre-mRNA splicing. May also be required for cell cycle progression at G2/M (By similarity).^[35] [RSMB_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [SMD2_YEAST] Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. [PRP8_YEAST] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.^{[36] [37] [38] [39]} [CWC25_YEAST] Involved in pre-mRNA splicing.^[40] [BUD31_YEAST] Involved in pre-mRNA splicing. Important for bud site selection. [SN309_YEAST] Involved in pre-mRNA splicing by stabilizing the NTC (or PRP19-associated complex). As a component of the NTC complex, associates to the spliceosome to mediate conformational rearrangement or to stabilize the structure of the spliceosome after U4 snRNA dissociation, which leads to spliceosome maturation.^{[41] [42]}

References

1. ↑ Schwer B, Guthrie C. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature. 1991 Feb 7;349(6309):494-9. PMID:1825134 doi:http://dx.doi.org/10.1038/349494a0
2. ↑ Chung S, McLean MR, Rymond BC. Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition. RNA. 1999 Aug;5(8):1042-54. PMID:10445879
3. ↑ Ben-Yehuda S, Dix I, Russell CS, McGarvey M, Beggs JD, Kupiec M. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics. 2000 Dec;156(4):1503-17. PMID:11102353
4. ↑ Russell CS, Ben-Yehuda S, Dix I, Kupiec M, Beggs JD. Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. RNA. 2000 Nov;6(11):1565-72. PMID:11105756
5. ↑ Zhu W, Rainville IR, Ding M, Bolus M, Heintz NH, Pederson DS. Evidence that the pre-mRNA splicing factor Clf1p plays a role in DNA replication in Saccharomyces cerevisiae. Genetics. 2002 Apr;160(4):1319-33. PMID:11973290
6. ↑ Wang Q, Hobbs K, Lynn B, Rymond BC. The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts. J Biol Chem. 2003 Mar 7;278(10):7875-83. Epub 2002 Dec 31. PMID:12509417 doi:http://dx.doi.org/10.1074/jbc.M210839200
7. ↑ Maeder C, Kutach AK, Guthrie C. ATP-dependent unwinding of U4/U6 snRNAs by the Brr2 helicase requires the C terminus of Prp8. Nat Struct Mol Biol. 2009 Jan;16(1):42-8. doi: 10.1038/nsmb.1535. Epub 2008 Dec, 21. PMID:19098916 doi:http://dx.doi.org/10.1038/nsmb.1535
8. ↑ Hahn D, Kudla G, Tollervey D, Beggs JD. Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning. Genes Dev. 2012 Nov 1;26(21):2408-21. doi: 10.1101/gad.199307.112. PMID:23124065 doi:http://dx.doi.org/10.1101/gad.199307.112
9. ↑ Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Luhrmann R, Wahl MC. Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase. Mol Cell. 2009 Aug 28;35(4):454-66. PMID:19716790 doi:10.1016/j.molcel.2009.08.006
10. ↑ Zhang L, Xu T, Maeder C, Bud LO, Shanks J, Nix J, Guthrie C, Pleiss JA, Zhao R. Structural evidence for consecutive Hel308-like modules in the spliceosomal ATPase Brr2. Nat Struct Mol Biol. 2009 Jul;16(7):731-9. Epub 2009 Jun 14. PMID:19525970 doi:10.1038/nsmb.1625
11. ↑ Xu D, Friesen JD. Splicing factor slt11p and its involvement in formation of U2/U6 helix II in activation of the yeast spliceosome. Mol Cell Biol. 2001 Feb;21(4):1011-23. PMID:11158289 doi:http://dx.doi.org/10.1128/MCB.21.4.1011-1023.2001
12. ↑ Xu D, Field DJ, Tang SJ, Moris A, Bobechko BP, Friesen JD. Synthetic lethality of yeast slt mutations with U2 small nuclear RNA mutations suggests functional interactions between U2 and U5 snRNPs that are important for both steps of pre-mRNA splicing. Mol Cell Biol. 1998 Apr;18(4):2055-66. PMID:9528778
13. ↑ Tsai WY, Chow YT, Chen HR, Huang KT, Hong RI, Jan SP, Kuo NY, Tsao TY, Chen CH, Cheng SC. Cef1p is a component of the Prp19p-associated complex and essential for pre-mRNA splicing. J Biol Chem. 1999 Apr 2;274(14):9455-62. PMID:10092627
14. ↑ Burns CG, Ohi R, Krainer AR, Gould KL. Evidence that Myb-related CDC5 proteins are required for pre-mRNA splicing. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13789-94. PMID:10570151
15. ↑ Burns CG, Ohi R, Mehta S, O'Toole ET, Winey M, Clark TA, Sugnet CW, Ares M Jr, Gould KL. Removal of a single alpha-tubulin gene intron suppresses cell cycle arrest phenotypes of splicing factor mutations in Saccharomyces cerevisiae. Mol Cell Biol. 2002 Feb;22(3):801-15. PMID:11784857
16. ↑ Ohi R, Feoktistova A, McCann S, Valentine V, Look AT, Lipsick JS, Gould KL. Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes. Mol Cell Biol. 1998 Jul;18(7):4097-108. PMID:9632794
17. ↑ Caspary F, Seraphin B. The yeast U2A'/U2B complex is required for pre-spliceosome formation. EMBO J. 1998 Nov 2;17(21):6348-58. PMID:9799242 doi:http://dx.doi.org/10.1093/emboj/17.21.6348
18. ↑ McGrail JC, Krause A, O'Keefe RT. The RNA binding protein Cwc2 interacts directly with the U6 snRNA to link the nineteen complex to the spliceosome during pre-mRNA splicing. Nucleic Acids Res. 2009 Jul;37(13):4205-17. Epub 2009 May 12. PMID:19435883 doi:http://dx.doi.org/gkp341
19. ↑ Rasche N, Dybkov O, Schmitzova J, Akyildiz B, Fabrizio P, Luhrmann R. Cwc2 and its human homologue RBM22 promote an active conformation of the spliceosome catalytic centre. EMBO J. 2012 Mar 21;31(6):1591-604. doi: 10.1038/emboj.2011.502. Epub 2012 Jan, 13. PMID:22246180 doi:http://dx.doi.org/10.1038/emboj.2011.502
20. ↑ Bordonne R, Tarassov I. The yeast SME1 gene encodes the homologue of the human E core protein. Gene. 1996 Oct 17;176(1-2):111-7. PMID:8918241
21. ↑ Seto AG, Zaug AJ, Sobel SG, Wolin SL, Cech TR. Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature. 1999 Sep 9;401(6749):177-80. PMID:10490028 doi:http://dx.doi.org/10.1038/43694
22. ↑ Rymond BC. Convergent transcripts of the yeast PRP38-SMD1 locus encode two essential splicing factors, including the D1 core polypeptide of small nuclear ribonucleoprotein particles. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):848-52. PMID:8430095
23. ↑ Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA. 2009 Dec;15(12):2174-85. Epub 2009 Sep 29. PMID:19789211 doi:http://dx.doi.org/rna.1790509
24. ↑ Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD. Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. RNA. 2009 Dec;15(12):2161-73. Epub 2009 Oct 23. PMID:19854871 doi:http://dx.doi.org/rna.1908309
25. ↑ Martinkova K, Lebduska P, Skruzny M, Folk P, Puta F. Functional mapping of Saccharomyces cerevisiae Prp45 identifies the SNW domain as essential for viability. J Biochem. 2002 Oct;132(4):557-63. PMID:12359070
26. ↑ Albers M, Diment A, Muraru M, Russell CS, Beggs JD. Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors. RNA. 2003 Jan;9(1):138-50. PMID:12554883
27. ↑ Seto AG, Zaug AJ, Sobel SG, Wolin SL, Cech TR. Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature. 1999 Sep 9;401(6749):177-80. PMID:10490028 doi:http://dx.doi.org/10.1038/43694
28. ↑ Roy J, Zheng B, Rymond BC, Woolford JL Jr. Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins. Mol Cell Biol. 1995 Jan;15(1):445-55. PMID:7799953
29. ↑ Tang J, Abovich N, Rosbash M. Identification and characterization of a yeast gene encoding the U2 small nuclear ribonucleoprotein particle B" protein. Mol Cell Biol. 1996 Jun;16(6):2787-95. PMID:8649387
30. ↑ Dix I, Russell C, Yehuda SB, Kupiec M, Beggs JD. The identification and characterization of a novel splicing protein, Isy1p, of Saccharomyces cerevisiae. RNA. 1999 Mar;5(3):360-8. PMID:10094305
31. ↑ Chen CH, Tsai WY, Chen HR, Wang CH, Cheng SC. Identification and characterization of two novel components of the Prp19p-associated complex, Ntc30p and Ntc20p. J Biol Chem. 2001 Jan 5;276(1):488-94. PMID:11018040 doi:http://dx.doi.org/10.1074/jbc.M006958200
32. ↑ Dahan O, Kupiec M. Mutations in genes of Saccharomyces cerevisiae encoding pre-mRNA splicing factors cause cell cycle arrest through activation of the spindle checkpoint. Nucleic Acids Res. 2002 Oct 15;30(20):4361-70. PMID:12384582
33. ↑ Ben-Yehuda S, Dix I, Russell CS, McGarvey M, Beggs JD, Kupiec M. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics. 2000 Dec;156(4):1503-17. PMID:11102353
34. ↑ Russell CS, Ben-Yehuda S, Dix I, Kupiec M, Beggs JD. Functional analyses of interacting factors involved in both pre-mRNA splicing and cell cycle progression in Saccharomyces cerevisiae. RNA. 2000 Nov;6(11):1565-72. PMID:11105756
35. ↑ Albers M, Diment A, Muraru M, Russell CS, Beggs JD. Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors. RNA. 2003 Jan;9(1):138-50. PMID:12554883
36. ↑ Jackson SP, Lossky M, Beggs JD. Cloning of the RNA8 gene of Saccharomyces cerevisiae, detection of the RNA8 protein, and demonstration that it is essential for nuclear pre-mRNA splicing. Mol Cell Biol. 1988 Mar;8(3):1067-75. PMID:2835658
37. ↑ Abovich N, Rosbash M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell. 1997 May 2;89(3):403-12. PMID:9150140
38. ↑ McPheeters DS, Muhlenkamp P. Spatial organization of protein-RNA interactions in the branch site-3' splice site region during pre-mRNA splicing in yeast. Mol Cell Biol. 2003 Jun;23(12):4174-86. PMID:12773561
39. ↑ Yang K, Zhang L, Xu T, Heroux A, Zhao R. Crystal structure of the beta-finger domain of Prp8 reveals analogy to ribosomal proteins. Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13817-22. Epub 2008 Sep 8. PMID:18779563
40. ↑ Hazbun TR, Malmstrom L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR 3rd, Davis TN. Assigning function to yeast proteins by integration of technologies. Mol Cell. 2003 Dec;12(6):1353-65. PMID:14690591
41. ↑ Chen HR, Tsao TY, Chen CH, Tsai WY, Her LS, Hsu MM, Cheng SC. Snt309p modulates interactions of Prp19p with its associated components to stabilize the Prp19p-associated complex essential for pre-mRNA splicing. Proc Natl Acad Sci U S A. 1999 May 11;96(10):5406-11. PMID:10318896
42. ↑ Chen HR, Jan SP, Tsao TY, Sheu YJ, Banroques J, Cheng SC. Snt309p, a component of the Prp19p-associated complex that interacts with Prp19p and associates with the spliceosome simultaneously with or immediately after dissociation of U4 in the same manner as Prp19p. Mol Cell Biol. 1998 Apr;18(4):2196-204. PMID:9528791
43. ↑ Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K. Cryo-EM structure of the spliceosome immediately after branching. Nature. 2016 Jul 26. doi: 10.1038/nature19316. PMID:27459055 doi:http://dx.doi.org/10.1038/nature19316