ID RRP4_YEAST Reviewed; 359 AA. AC P38792; D3DL18; DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-1995, sequence version 1. DT 27-MAR-2024, entry version 186. DE RecName: Full=Exosome complex component RRP4; DE AltName: Full=Ribosomal RNA-processing protein 4; GN Name=RRP4; OrderedLocusNames=YHR069C; OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; OC Saccharomycetales; Saccharomycetaceae; Saccharomyces. OX NCBI_TaxID=559292; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 94-101; 256-271 AND RP 306-318, FUNCTION, SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY. RX PubMed=9390555; DOI=10.1016/s0092-8674(00)80432-8; RA Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.; RT "The exosome: a conserved eukaryotic RNA processing complex containing RT multiple 3'-->5' exoribonucleases."; RL Cell 91:457-466(1997). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=8091229; DOI=10.1126/science.8091229; RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J., RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., RA Waterston R., Wilson R., Vaudin M.; RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome RT VIII."; RL Science 265:2077-2082(1994). RN [3] RP GENOME REANNOTATION. RC STRAIN=ATCC 204508 / S288c; RX PubMed=24374639; DOI=10.1534/g3.113.008995; RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now."; RL G3 (Bethesda) 4:389-398(2014). RN [4] RP FUNCTION, AND MUTAGENESIS OF LEU-136. RX PubMed=8600032; DOI=10.1101/gad.10.4.502; RA Mitchell P., Petfalski E., Tollervey D.; RT "The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing RT mechanism."; RL Genes Dev. 10:502-513(1996). RN [5] RP IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY, AND RP SUBCELLULAR LOCATION. RX PubMed=10465791; DOI=10.1101/gad.13.16.2148; RA Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., RA Mitchell P.; RT "The yeast exosome and human PM-Scl are related complexes of 3'-->5' RT exonucleases."; RL Genes Dev. 13:2148-2158(1999). RN [6] RP INTERACTION WITH LRP1. RX PubMed=12972615; DOI=10.1128/mcb.23.19.6982-6992.2003; RA Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M., RA Tollervey D.; RT "Rrp47p is an exosome-associated protein required for the 3' processing of RT stable RNAs."; RL Mol. Cell. Biol. 23:6982-6992(2003). RN [7] RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]. RX PubMed=14562095; DOI=10.1038/nature02026; RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., RA Weissman J.S., O'Shea E.K.; RT "Global analysis of protein localization in budding yeast."; RL Nature 425:686-691(2003). RN [8] RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS]. RX PubMed=14562106; DOI=10.1038/nature02046; RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., RA O'Shea E.K., Weissman J.S.; RT "Global analysis of protein expression in yeast."; RL Nature 425:737-741(2003). RN [9] RP RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE RP ACTIVITY. RX PubMed=17174896; DOI=10.1016/j.cell.2006.10.037; RA Liu Q., Greimann J.C., Lima C.D.; RT "Reconstitution, activities, and structure of the eukaryotic RNA exosome."; RL Cell 127:1223-1237(2006). RN [10] RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION OF THE EXOSOME RP WITH RRP6 AND SKI7, AND SUBUNIT. RX PubMed=17173052; DOI=10.1038/nsmb1184; RA Dziembowski A., Lorentzen E., Conti E., Seraphin B.; RT "A single subunit, Dis3, is essentially responsible for yeast exosome core RT activity."; RL Nat. Struct. Mol. Biol. 14:15-22(2007). RN [11] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-28 AND SER-268, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200; RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.; RT "A multidimensional chromatography technology for in-depth phosphoproteome RT analysis."; RL Mol. Cell. Proteomics 7:1389-1396(2008). RN [12] RP FUNCTION IN RNA EXOSOME COMPLEX STABILITY. RX PubMed=19060898; DOI=10.1038/nsmb.1528; RA Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., RA Sanchez-Rotunno M., Arraiano C.M., van Hoof A.; RT "The exosome contains domains with specific endoribonuclease, RT exoribonuclease and cytoplasmic mRNA decay activities."; RL Nat. Struct. Mol. Biol. 16:56-62(2009). RN [13] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-28, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19779198; DOI=10.1126/science.1172867; RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.; RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights RT into evolution."; RL Science 325:1682-1686(2009). RN [14] RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY RP [LARGE SCALE ANALYSIS]. RX PubMed=22814378; DOI=10.1073/pnas.1210303109; RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.; RT "N-terminal acetylome analyses and functional insights of the N-terminal RT acetyltransferase NatB."; RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012). CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has CC 3'->5' exoribonuclease activity and participates in a multitude of CC cellular RNA processing and degradation events. In the nucleus, the RNA CC exosome complex is involved in proper maturation of stable RNA species CC such as rRNA, snRNA and snoRNA, in the elimination of RNA processing CC by-products and non-coding 'pervasive' transcripts, such as antisense CC RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with CC processing defects, thereby limiting or excluding their export to the CC cytoplasm. In the cytoplasm, the RNA exosome complex is involved in CC general mRNA turnover and in RNA surveillance pathways, preventing CC translation of aberrant mRNAs. The catalytic inactive RNA exosome core CC complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the CC binding and presentation of RNA for ribonucleolysis, and to serve as a CC scaffold for the association with catalytic subunits and accessory CC proteins or complexes. RRP4 as peripheral part of the Exo-9 complex is CC thought to stabilize the hexameric ring of RNase PH-domain subunits. CC {ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:19060898, CC ECO:0000269|PubMed:8600032, ECO:0000269|PubMed:9390555}. CC -!- SUBUNIT: Component of the RNA exosome complex. Specifically part of the CC catalytically inactive RNA exosome core (Exo-9) complex which CC associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and CC nuclear-specific RNA exosome complex forms. Exo-9 is formed by a CC hexameric ring of RNase PH domain-containing subunits and peripheral S1 CC domain-containing components CSL4, RRP4 and RRP40 located on the top of CC the ring structure. Interacts with LRP1/RRP47. CC {ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:12972615, CC ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:9390555}. CC -!- INTERACTION: CC P38792; P53859: CSL4; NbExp=15; IntAct=EBI-1757, EBI-1731; CC P38792; Q08162: DIS3; NbExp=5; IntAct=EBI-1757, EBI-1740; CC P38792; P46948: SKI6; NbExp=4; IntAct=EBI-1757, EBI-1788; CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. CC -!- MISCELLANEOUS: Present with 4840 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: Belongs to the RRP4 family. {ECO:0000305}. CC -!- CAUTION: Was originally (PubMed:9390555, PubMed:8600032) thought to CC have exonuclease activity but it was later shown (PubMed:17173052, CC PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has CC this activity. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; U00061; AAB68393.1; -; Genomic_DNA. DR EMBL; BK006934; DAA06762.1; -; Genomic_DNA. DR PIR; S46714; S46714. DR RefSeq; NP_011936.1; NM_001179199.1. DR PDB; 4IFD; X-ray; 2.80 A; H=1-359. DR PDB; 4OO1; X-ray; 3.30 A; H=1-359. DR PDB; 5C0W; X-ray; 4.60 A; H=1-359. DR PDB; 5C0X; X-ray; 3.81 A; H=1-359. DR PDB; 5G06; EM; 4.20 A; H=1-359. DR PDB; 5JEA; X-ray; 2.65 A; H=50-359. DR PDB; 5K36; X-ray; 3.10 A; H=1-359. DR PDB; 5OKZ; X-ray; 3.20 A; H/R/b/l=50-359. DR PDB; 5VZJ; X-ray; 3.30 A; H=1-359. DR PDB; 6FSZ; EM; 4.60 A; HH=1-359. DR PDB; 6LQS; EM; 3.80 A; r4=1-359. DR PDB; 7AJT; EM; 4.60 A; EI=1-359. DR PDB; 7AJU; EM; 3.80 A; EI=1-359. DR PDB; 7D4I; EM; 4.00 A; r4=1-359. DR PDBsum; 4IFD; -. DR PDBsum; 4OO1; -. DR PDBsum; 5C0W; -. DR PDBsum; 5C0X; -. DR PDBsum; 5G06; -. DR PDBsum; 5JEA; -. DR PDBsum; 5K36; -. DR PDBsum; 5OKZ; -. DR PDBsum; 5VZJ; -. DR PDBsum; 6FSZ; -. DR PDBsum; 6LQS; -. DR PDBsum; 7AJT; -. DR PDBsum; 7AJU; -. DR PDBsum; 7D4I; -. DR AlphaFoldDB; P38792; -. DR EMDB; EMD-0952; -. DR EMDB; EMD-11807; -. DR EMDB; EMD-11808; -. DR EMDB; EMD-30574; -. DR EMDB; EMD-4301; -. DR SMR; P38792; -. DR BioGRID; 36501; 324. DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant. DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant. DR DIP; DIP-5888N; -. DR IntAct; P38792; 23. DR MINT; P38792; -. DR STRING; 4932.YHR069C; -. DR iPTMnet; P38792; -. DR MaxQB; P38792; -. DR PaxDb; 4932-YHR069C; -. DR PeptideAtlas; P38792; -. DR EnsemblFungi; YHR069C_mRNA; YHR069C; YHR069C. DR GeneID; 856466; -. DR KEGG; sce:YHR069C; -. DR AGR; SGD:S000001111; -. DR SGD; S000001111; RRP4. DR VEuPathDB; FungiDB:YHR069C; -. DR eggNOG; KOG3013; Eukaryota. DR GeneTree; ENSGT00940000153596; -. DR HOGENOM; CLU_034114_3_0_1; -. DR InParanoid; P38792; -. DR OMA; GVNGFIW; -. DR OrthoDB; 5472588at2759; -. DR BioCyc; YEAST:G3O-31119-MONOMER; -. DR Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease. DR Reactome; R-SCE-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA. DR Reactome; R-SCE-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA. DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol. DR BioGRID-ORCS; 856466; 1 hit in 10 CRISPR screens. DR PRO; PR:P38792; -. DR Proteomes; UP000002311; Chromosome VIII. DR RNAct; P38792; Protein. DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD. DR GO; GO:0000178; C:exosome (RNase complex); IPI:ComplexPortal. DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD. DR GO; GO:0005730; C:nucleolus; IDA:ComplexPortal. DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal. DR GO; GO:0003723; F:RNA binding; IBA:GO_Central. DR GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central. DR GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central. DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD. DR GO; GO:0071028; P:nuclear mRNA surveillance; IGI:SGD. DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD. DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD. DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IMP:SGD. DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD. DR GO; GO:0006401; P:RNA catabolic process; IDA:ComplexPortal. DR GO; GO:0006396; P:RNA processing; IDA:ComplexPortal. DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD. DR CDD; cd22525; KH-I_Rrp4_eukar; 1. DR CDD; cd05789; S1_Rrp4; 1. DR Gene3D; 2.40.50.100; -; 1. DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1. DR InterPro; IPR025721; Exosome_cplx_N_dom. DR InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4. DR InterPro; IPR004088; KH_dom_type_1. DR InterPro; IPR036612; KH_dom_type_1_sf. DR InterPro; IPR012340; NA-bd_OB-fold. DR InterPro; IPR048565; RRP4_S1. DR PANTHER; PTHR21321:SF4; EXOSOME COMPLEX COMPONENT RRP4; 1. DR PANTHER; PTHR21321; PNAS-3 RELATED; 1. DR Pfam; PF14382; ECR1_N; 1. DR Pfam; PF15985; KH_6; 1. DR Pfam; PF21266; RRP4_S1; 1. DR SUPFAM; SSF54791; Eukaryotic type KH-domain (KH-domain type I); 1. DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1. DR SUPFAM; SSF110324; Ribosomal L27 protein-like; 1. PE 1: Evidence at protein level; KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing; Exosome; KW Nucleus; Phosphoprotein; Reference proteome; RNA-binding; rRNA processing. FT INIT_MET 1 FT /note="Removed" FT /evidence="ECO:0007744|PubMed:22814378" FT CHAIN 2..359 FT /note="Exosome complex component RRP4" FT /id="PRO_0000097455" FT DOMAIN 107..187 FT /note="S1 motif" FT REGION 242..266 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOD_RES 2 FT /note="N-acetylserine" FT /evidence="ECO:0007744|PubMed:22814378" FT MOD_RES 28 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:18407956, FT ECO:0007744|PubMed:19779198" FT MOD_RES 268 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:18407956" FT MUTAGEN 136 FT /note="L->P: In RRP4-1; temperature-sensitive(ts) lethal FT mutation." FT /evidence="ECO:0000269|PubMed:8600032" FT STRAND 7..12 FT /evidence="ECO:0007829|PDB:4IFD" FT STRAND 60..63 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 65..69 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 73..76 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 79..91 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 94..101 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 111..119 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 121..127 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 129..132 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 134..137 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 138..140 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 146..148 FT /evidence="ECO:0007829|PDB:4IFD" FT STRAND 151..153 FT /evidence="ECO:0007829|PDB:5K36" FT HELIX 154..157 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 159..162 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 168..176 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 178..180 FT /evidence="ECO:0007829|PDB:4IFD" FT STRAND 182..185 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 188..193 FT /evidence="ECO:0007829|PDB:4IFD" FT STRAND 196..201 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 204..206 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 213..217 FT /evidence="ECO:0007829|PDB:5JEA" FT TURN 218..220 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 221..225 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 229..235 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 238..241 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 244..248 FT /evidence="ECO:0007829|PDB:4OO1" FT HELIX 270..276 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 279..281 FT /evidence="ECO:0007829|PDB:4IFD" FT HELIX 291..309 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 316..326 FT /evidence="ECO:0007829|PDB:5JEA" FT STRAND 329..331 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 332..336 FT /evidence="ECO:0007829|PDB:5JEA" FT HELIX 338..354 FT /evidence="ECO:0007829|PDB:5JEA" SQ SEQUENCE 359 AA; 39427 MW; 0718A7ABF42E9B9B CRC64; MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES DSQIVTPGEL VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL KGRYAPETGD HVVGRIAEVG NKRWKVDIGG KQHAVLMLGS VNLPGGILRR KSESDELQMR SFLKEGDLLN AEVQSLFQDG SASLHTRSLK YGKLRNGMFC QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD LARDTPSANN SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT AEKMRGNGN //