6em5

Structural highlights

Function

[HAS1_YEAST] ATP-dependent RNA helicase involved in 40S ribosomal subunit biogenesis. Required for the processing and cleavage of 35S pre-rRNA at sites A0, A1, and A2, leading to mature 18S rRNA.^{[1] [2] [3]} [ERB1_YEAST] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03027]^{[4] [5]} [RL36B_YEAST] Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel.^[6] [RL37A_YEAST] Binds to the 23S rRNA (By similarity). [BRX1_YEAST] Required for biogenesis of the 60S ribosomal subunit.^[7] [YTM1_YEAST] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03029]^{[8] [9] [10]} [RL4A_YEAST] Participates in the regulation of the accumulation of its own mRNA.^[11] [NUG1_YEAST] GTPase required for 60S ribosomal subunit export to the cytoplasm.^[12] [NOC3_YEAST] Required for synthesis of 60S ribosomal subunits and the transport of pre-ribosomes from the nucleoplasm to the cytoplasm. Also required for initiation of DNA replication. May function downstream of the origin recognition complex (ORC complex) in the loading of CDC6 and the minichromosome maintenance complex (MCM complex) onto chromatin during the G1 phase of the cell cycle. Essential for growth.^{[13] [14]} [RL25_YEAST] This protein binds to a specific region on the 26S rRNA. [CIC1_YEAST] An adapter protein that specifically links the 26S proteasome to its substrate CDC4 which is one of the substrate recognition subunits of the SCF E3 ubiquitin ligase complex. Required for turnover of cell cycle regulatory proteins CDC4 and GRR1. Required for synthesis and nuclear export of 60S ribosomal subunits. Required for vegetative growth.^{[15] [16]} [NIP7_YEAST] Required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly. [RRP1_YEAST] Required for 27S rRNA processing to 25S and 5.8S. [SPB1_YEAST] Required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation. Methylates also the uridine in position 2921 in the absence of methylation of this residue guided by snoRNA snR52 at the stage of 35S pre-rRNA maturation.[HAMAP-Rule:MF_03163]^{[17] [18] [19]} [IF6_YEAST] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. Is also involved in ribosome biogenesis. Associates with pre-60S subunits in the nucleus and is involved in its nuclear export. Cytoplasmic release of TIF6 from 60S subunits and nuclear relocalization is promoted by the GTPase RIA1/EFL1 and by SDO1. Also required for pre-rRNA processing.^{[20] [21] [22] [23] [24] [25]} [RLP24_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Ensures the docking of NOG1 to pre-60S particles.^[26] [EBP2_YEAST] Required for the processing of the 27S pre-rRNA. Probably involved in the step of the processing of the 27 SA precursor into the 27 SB intermediate.^{[27] [28]} [NSA2_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. May play a part in the quality control of pre-60S particles. Under normal, rapid growth conditions, high levels of NSA2 would allow the progression of pre-60S particles through the ITS2 processing.^{[29] [30]} [NOG1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.^[31] [RPF1_YEAST] Essential protein. Required for biogenesis of the 60S ribosomal subunit.^{[32] [33]} [RLP7_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. May act as a specificity factor that binds precursor rRNAs and tethers the enzymes that carry out the early 5' to 3' exonucleolytic reactions that generate the mature rRNAs.^[34] [NOP16_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.^[35] [MAK16_YEAST] Its role might be as part of the apparatus concerned with the nuclear events of the cell cycle.^[36] [PESC_YEAST] Component of the NOP7 complex, which is required for maturation of the 25S and 5.8S ribosomal RNAs and formation of the 60S ribosome.[HAMAP-Rule:MF_03028]^{[37] [38] [39] [40]} [MRT4_YEAST] Involved in mRNA turnover and ribosome assembly. [NOP2_YEAST] S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA. Required for 60S ribosomal subunit synthesis and processing.^{[41] [42]} [NOP15_YEAST] Involved in the biogenesis of the 60S ribosomal subunit. Required for pre-rRNA processing and cytokinesis. Associates with the precursors of the 25S and 5.8S rRNAs.^{[43] [44]} [NSA1_YEAST] Involved in the biogenesis of the 60S ribosomal subunit.^[45]

See Also

• Eukaryotic initiation factor 3D structures
• Ribosome 3D structures
• Ribosome biogenesis protein

References

1. ↑ Emery B, de la Cruz J, Rocak S, Deloche O, Linder P. Has1p, a member of the DEAD-box family, is required for 40S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Mol Microbiol. 2004 Apr;52(1):141-58. doi: 10.1111/j.1365-2958.2003.03973.x. PMID:15049817 doi:http://dx.doi.org/10.1111/j.1365-2958.2003.03973.x
2. ↑ Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004 Jul 9;118(1):31-44. PMID:15242642 doi:10.1016/j.cell.2004.06.013
3. ↑ Rocak S, Emery B, Tanner NK, Linder P. Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs. Nucleic Acids Res. 2005 Feb 17;33(3):999-1009. doi: 10.1093/nar/gki244. Print, 2005. PMID:15718299 doi:http://dx.doi.org/10.1093/nar/gki244
4. ↑ Pestov DG, Stockelman MG, Strezoska Z, Lau LF. ERB1, the yeast homolog of mammalian Bop1, is an essential gene required for maturation of the 25S and 5.8S ribosomal RNAs. Nucleic Acids Res. 2001 Sep 1;29(17):3621-30. PMID:11522832
5. ↑ Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford JL Jr. Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. Mol Biol Cell. 2008 Jul;19(7):2844-56. doi: 10.1091/mbc.E07-12-1281. Epub 2008, Apr 30. PMID:18448671 doi:http://dx.doi.org/10.1091/mbc.E07-12-1281
6. ↑ Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M. The structure of the eukaryotic ribosome at 3.0 A resolution. Science. 2011 Dec 16;334(6062):1524-9. Epub 2011 Nov 17. PMID:22096102 doi:10.1126/science.1212642
7. ↑ Kaser A, Bogengruber E, Hallegger M, Doppler E, Lepperdinger G, Jantsch M, Breitenbach M, Kreil G. Brix from xenopus laevis and brx1p from yeast define a new family of proteins involved in the biogenesis of large ribosomal subunits. Biol Chem. 2001 Dec;382(12):1637-47. doi: 10.1515/BC.2001.199. PMID:11843177 doi:http://dx.doi.org/10.1515/BC.2001.199
8. ↑ Miles TD, Jakovljevic J, Horsey EW, Harnpicharnchai P, Tang L, Woolford JL Jr. Ytm1, Nop7, and Erb1 form a complex necessary for maturation of yeast 66S preribosomes. Mol Cell Biol. 2005 Dec;25(23):10419-32. doi: 10.1128/MCB.25.23.10419-10432.2005. PMID:16287855 doi:http://dx.doi.org/10.1128/MCB.25.23.10419-10432.2005
9. ↑ Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford JL Jr. Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. Mol Biol Cell. 2008 Jul;19(7):2844-56. doi: 10.1091/mbc.E07-12-1281. Epub 2008, Apr 30. PMID:18448671 doi:http://dx.doi.org/10.1091/mbc.E07-12-1281
10. ↑ Bassler J, Kallas M, Pertschy B, Ulbrich C, Thoms M, Hurt E. The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly. Mol Cell. 2010 Jun 11;38(5):712-21. doi: 10.1016/j.molcel.2010.05.024. PMID:20542003 doi:http://dx.doi.org/10.1016/j.molcel.2010.05.024
11. ↑ Presutti C, Ciafre SA, Bozzoni I. The ribosomal protein L2 in S. cerevisiae controls the level of accumulation of its own mRNA. EMBO J. 1991 Aug;10(8):2215-21. PMID:2065661
12. ↑ Bassler J, Grandi P, Gadal O, Lessmann T, Petfalski E, Tollervey D, Lechner J, Hurt E. Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol Cell. 2001 Sep;8(3):517-29. PMID:11583615
13. ↑ Milkereit P, Gadal O, Podtelejnikov A, Trumtel S, Gas N, Petfalski E, Tollervey D, Mann M, Hurt E, Tschochner H. Maturation and intranuclear transport of pre-ribosomes requires Noc proteins. Cell. 2001 May 18;105(4):499-509. PMID:11371346
14. ↑ Zhang Y, Yu Z, Fu X, Liang C. Noc3p, a bHLH protein, plays an integral role in the initiation of DNA replication in budding yeast. Cell. 2002 Jun 28;109(7):849-60. PMID:12110182
15. ↑ Jager S, Strayle J, Heinemeyer W, Wolf DH. Cic1, an adaptor protein specifically linking the 26S proteasome to its substrate, the SCF component Cdc4. EMBO J. 2001 Aug 15;20(16):4423-31. PMID:11500370 doi:http://dx.doi.org/10.1093/emboj/20.16.4423
16. ↑ Fatica A, Oeffinger M, Tollervey D, Bozzoni I. Cic1p/Nsa3p is required for synthesis and nuclear export of 60S ribosomal subunits. RNA. 2003 Dec;9(12):1431-6. PMID:14623999
17. ↑ Kressler D, Rojo M, Linder P, Cruz J. Spb1p is a putative methyltransferase required for 60S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Nucleic Acids Res. 1999 Dec 1;27(23):4598-608. PMID:10556316
18. ↑ Bonnerot C, Pintard L, Lutfalla G. Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. Mol Cell. 2003 Nov;12(5):1309-15. PMID:14636587
19. ↑ Lapeyre B, Purushothaman SK. Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol Cell. 2004 Nov 19;16(4):663-9. PMID:15546625 doi:http://dx.doi.org/S1097276504006483
20. ↑ Sanvito F, Piatti S, Villa A, Bossi M, Lucchini G, Marchisio PC, Biffo S. The beta4 integrin interactor p27(BBP/eIF6) is an essential nuclear matrix protein involved in 60S ribosomal subunit assembly. J Cell Biol. 1999 Mar 8;144(5):823-37. PMID:10085284
21. ↑ Senger B, Lafontaine DL, Graindorge JS, Gadal O, Camasses A, Sanni A, Garnier JM, Breitenbach M, Hurt E, Fasiolo F. The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis. Mol Cell. 2001 Dec;8(6):1363-73. PMID:11779510
22. ↑ Basu U, Si K, Warner JR, Maitra U. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol Cell Biol. 2001 Mar;21(5):1453-62. PMID:11238882 doi:10.1128/MCB.21.5.1453-1462.2001
23. ↑ Menne TF, Goyenechea B, Sanchez-Puig N, Wong CC, Tonkin LM, Ancliff PJ, Brost RL, Costanzo M, Boone C, Warren AJ. The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. Nat Genet. 2007 Apr;39(4):486-95. Epub 2007 Mar 11. PMID:17353896 doi:ng1994
24. ↑ Ray P, Basu U, Ray A, Majumdar R, Deng H, Maitra U. The Saccharomyces cerevisiae 60 S ribosome biogenesis factor Tif6p is regulated by Hrr25p-mediated phosphorylation. J Biol Chem. 2008 Apr 11;283(15):9681-91. doi: 10.1074/jbc.M710294200. Epub 2008 , Feb 5. PMID:18256024 doi:10.1074/jbc.M710294200
25. ↑ Groft CM, Beckmann R, Sali A, Burley SK. Crystal structures of ribosome anti-association factor IF6. Nat Struct Biol. 2000 Dec;7(12):1156-64. PMID:11101899 doi:10.1038/82017
26. ↑ Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M. Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol. 2003 Jul;23(13):4449-60. PMID:12808088
27. ↑ Huber MD, Dworet JH, Shire K, Frappier L, McAlear MA. The budding yeast homolog of the human EBNA1-binding protein 2 (Ebp2p) is an essential nucleolar protein required for pre-rRNA processing. J Biol Chem. 2000 Sep 15;275(37):28764-73. doi: 10.1074/jbc.M000594200. PMID:10849420 doi:http://dx.doi.org/10.1074/jbc.M000594200
28. ↑ Tsujii R, Miyoshi K, Tsuno A, Matsui Y, Toh-e A, Miyakawa T, Mizuta K. Ebp2p, yeast homologue of a human protein that interacts with Epstein-Barr virus nuclear antigen 1, is required for pre-rRNA processing and ribosomal subunit assembly. Genes Cells. 2000 Jul;5(7):543-53. PMID:10947841
29. ↑ Wade CH, Umbarger MA, McAlear MA. The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast. 2006 Mar;23(4):293-306. PMID:16544271 doi:http://dx.doi.org/10.1002/yea.1353
30. ↑ Lebreton A, Saveanu C, Decourty L, Jacquier A, Fromont-Racine M. Nsa2 is an unstable, conserved factor required for the maturation of 27 SB pre-rRNAs. J Biol Chem. 2006 Sep 15;281(37):27099-108. Epub 2006 Jul 21. PMID:16861225 doi:http://dx.doi.org/M602199200
31. ↑ Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M. Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol. 2003 Jul;23(13):4449-60. PMID:12808088
32. ↑ Wehner KA, Baserga SJ. The sigma(70)-like motif: a eukaryotic RNA binding domain unique to a superfamily of proteins required for ribosome biogenesis. Mol Cell. 2002 Feb;9(2):329-39. PMID:11864606
33. ↑ Bogengruber E, Briza P, Doppler E, Wimmer H, Koller L, Fasiolo F, Senger B, Hegemann JH, Breitenbach M. Functional analysis in yeast of the Brix protein superfamily involved in the biogenesis of ribosomes. FEMS Yeast Res. 2003 Mar;3(1):35-43. PMID:12702244
34. ↑ Dunbar DA, Dragon F, Lee SJ, Baserga SJ. A nucleolar protein related to ribosomal protein L7 is required for an early step in large ribosomal subunit biogenesis. Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13027-32. PMID:11087857 doi:http://dx.doi.org/10.1073/pnas.97.24.13027
35. ↑ Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M, Meagher D, Imai B, Guo Y, Brame CJ, Shabanowitz J, Hunt DF, Woolford JL Jr. Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell. 2001 Sep;8(3):505-15. PMID:11583614
36. ↑ Wickner RB. Host function of MAK16: G1 arrest by a mak16 mutant of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1988 Aug;85(16):6007-11. PMID:3045810
37. ↑ Adams CC, Jakovljevic J, Roman J, Harnpicharnchai P, Woolford JL Jr. Saccharomyces cerevisiae nucleolar protein Nop7p is necessary for biogenesis of 60S ribosomal subunits. RNA. 2002 Feb;8(2):150-65. PMID:11911362
38. ↑ Oeffinger M, Leung A, Lamond A, Tollervey D. Yeast Pescadillo is required for multiple activities during 60S ribosomal subunit synthesis. RNA. 2002 May;8(5):626-36. PMID:12022229
39. ↑ Du YC, Stillman B. Yph1p, an ORC-interacting protein: potential links between cell proliferation control, DNA replication, and ribosome biogenesis. Cell. 2002 Jun 28;109(7):835-48. PMID:12110181
40. ↑ Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford JL Jr. Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. Mol Biol Cell. 2008 Jul;19(7):2844-56. doi: 10.1091/mbc.E07-12-1281. Epub 2008, Apr 30. PMID:18448671 doi:http://dx.doi.org/10.1091/mbc.E07-12-1281
41. ↑ Sharma S, Yang J, Watzinger P, Kotter P, Entian KD. Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Nucleic Acids Res. 2013 Oct;41(19):9062-76. doi: 10.1093/nar/gkt679. Epub 2013, Aug 2. PMID:23913415 doi:http://dx.doi.org/10.1093/nar/gkt679
42. ↑ King M, Ton D, Redman KL. A conserved motif in the yeast nucleolar protein Nop2p contains an essential cysteine residue. Biochem J. 1999 Jan 1;337 ( Pt 1):29-35. PMID:9854021
43. ↑ Harnpicharnchai P, Jakovljevic J, Horsey E, Miles T, Roman J, Rout M, Meagher D, Imai B, Guo Y, Brame CJ, Shabanowitz J, Hunt DF, Woolford JL Jr. Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell. 2001 Sep;8(3):505-15. PMID:11583614
44. ↑ Oeffinger M, Tollervey D. Yeast Nop15p is an RNA-binding protein required for pre-rRNA processing and cytokinesis. EMBO J. 2003 Dec 15;22(24):6573-83. PMID:14657029 doi:http://dx.doi.org/10.1093/emboj/cdg616
45. ↑ Wade CH, Umbarger MA, McAlear MA. The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes. Yeast. 2006 Mar;23(4):293-306. PMID:16544271 doi:http://dx.doi.org/10.1002/yea.1353
46. ↑ Kater L, Thoms M, Barrio-Garcia C, Cheng J, Ismail S, Ahmed YL, Bange G, Kressler D, Berninghausen O, Sinning I, Hurt E, Beckmann R. Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell. 2017 Dec 14;171(7):1599-1610.e14. doi: 10.1016/j.cell.2017.11.039. PMID:29245012 doi:http://dx.doi.org/10.1016/j.cell.2017.11.039