6j6q

Structural highlights

Function

[YJU2_YEAST] Part of the spliceosome which catalyzes two sequential transesterification reactions, first the excision of the non-coding intron from pre-mRNA and then the ligation of the coding exons to form the mature mRNA (PubMed:19935684, PubMed:27445308, PubMed:27459055, PubMed:29146871). Plays a role (via N-terminus) in stabilizing the structure of the spliceosome catalytic core and docking of the branch helix into the active site, producing 5'-exon and lariat intron-3'-intermediates (PubMed:23438600, PubMed:27459055). Further stabilizes spliceosome conformation for 3'-splice site docking (via C-terminus) promoting exon ligation (PubMed:29146871).[HAMAP-Rule:MF_03226]^{[1] [2] [3] [4] [5]} [MSL1_YEAST] Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA.^[6] [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.^{[7] [8]} [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. [SN114_YEAST] Component of the U5 snRNP complex required for pre-mRNA splicing. Binds GTP. [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.^{[9] [10] [11] [12]} [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.^{[13] [14]} [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. [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.^{[15] [16]} [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. [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.^{[17] [18]} [PRP17_YEAST] May function in the second step of pre-mRNA splicing. Regulatory protein involved in replication and mitotic spindle formation and/or maintenance. Required for initiation and completion of S-phase and for initiation and completion of DNA replication. Might be required for the maintenance of microtubules. Essential only at elevated temperatures. [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.^[19] [CWC22_YEAST] May be involved in pre-mRNA splicing. [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. [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.^{[20] [21] [22] [23]} [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.^[24] [SYF2_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.^{[25] [26] [27]} [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.^{[28] [29]} [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. [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.^{[30] [31]} [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.^{[32] [33]} [BUD31_YEAST] Involved in pre-mRNA splicing. Important for bud site selection. [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).^{[34] [35] [36] [37] [38]} [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.^{[39] [40] [41]} [CWC15_YEAST] Involved in pre-mRNA splicing. [PRP46_YEAST] Involved in pre-mRNA splicing. May also be required for cell cycle progression at G2/M (By similarity).^[42] [PRP45_YEAST] Involved in pre-mRNA splicing. Associated with the spliceosome throughout the splicing reactions, until after the second catalytic step.^{[43] [44]}

See Also

• Nucleoprotein 3D structures
• Pre-mRNA splicing factors 3D structures

References

1. ↑ Warkocki Z, Odenwalder P, Schmitzova J, Platzmann F, Stark H, Urlaub H, Ficner R, Fabrizio P, Luhrmann R. Reconstitution of both steps of Saccharomyces cerevisiae splicing with purified spliceosomal components. Nat Struct Mol Biol. 2009 Dec;16(12):1237-43. Epub 2009 Nov 22. PMID:19935684 doi:http://dx.doi.org/nsmb.1729
2. ↑ Chiang TW, Cheng SC. A weak spliceosome-binding domain of Yju2 functions in the first step and bypasses Prp16 in the second step of splicing. Mol Cell Biol. 2013 May;33(9):1746-55. doi: 10.1128/MCB.00035-13. Epub 2013 Feb, 25. PMID:23438600 doi:http://dx.doi.org/10.1128/MCB.00035-13
3. ↑ Wan R, Yan C, Bai R, Huang G, Shi Y. Structure of a yeast catalytic step I spliceosome at 3.4 A resolution. Science. 2016 Aug 26;353(6302):895-904. doi: 10.1126/science.aag2235. Epub 2016, Jul 21. PMID:27445308 doi:http://dx.doi.org/10.1126/science.aag2235
4. ↑ 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
5. ↑ Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K. Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Science. 2017 Dec 8;358(6368):1283-1288. doi: 10.1126/science.aar3729. Epub 2017 , Nov 16. PMID:29146871 doi:http://dx.doi.org/10.1126/science.aar3729
6. ↑ 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
7. ↑ 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
8. ↑ 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
9. ↑ 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
10. ↑ 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
11. ↑ 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
12. ↑ 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
13. ↑ 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
14. ↑ 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
15. ↑ 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
16. ↑ 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
17. ↑ 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
18. ↑ 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
19. ↑ 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
20. ↑ 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
21. ↑ 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
22. ↑ 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
23. ↑ 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
24. ↑ 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
25. ↑ 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
26. ↑ 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
27. ↑ 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
28. ↑ 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
29. ↑ 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
30. ↑ 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
31. ↑ 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
32. ↑ 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
33. ↑ 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
34. ↑ 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
35. ↑ 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
36. ↑ 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
37. ↑ 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
38. ↑ 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
39. ↑ 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
40. ↑ 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
41. ↑ 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
42. ↑ 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
43. ↑ 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
44. ↑ 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
45. ↑ Wan R, Bai R, Yan C, Lei J, Shi Y. Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell. 2019 Apr 4;177(2):339-351.e13. doi: 10.1016/j.cell.2019.02.006. Epub 2019, Mar 14. PMID:30879786 doi:http://dx.doi.org/10.1016/j.cell.2019.02.006