RRP4_YEAST
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 03-AUG-2022, entry version 179.
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 VARIANT RRP4-1.
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 and PubMed:8600032) thought to
CC have exonuclease activity but it was later shown (PubMed:17173052 and
CC PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has
CC this activity. {ECO:0000305}.
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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 SMR; P38792; -.
DR BioGRID; 36501; 290.
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; P38792; -.
DR PRIDE; P38792; -.
DR EnsemblFungi; YHR069C_mRNA; YHR069C; YHR069C.
DR GeneID; 856466; -.
DR KEGG; sce:YHR069C; -.
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 BioCyc; YEAST:G3O-31119-MON; -.
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 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:0070651; P:nonfunctional rRNA decay; IC:SGD.
DR GO; GO:0071028; P:nuclear mRNA surveillance; IGI:SGD.
DR GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC: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:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC:SGD.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IMP:SGD.
DR GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IC: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 Gene3D; 2.40.50.140; -; 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 PANTHER; PTHR21321; PTHR21321; 1.
DR Pfam; PF14382; ECR1_N; 1.
DR Pfam; PF15985; KH_6; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 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 VARIANT 136
FT /note="L -> P (in RRP4-1; temperature-sensitive(ts) lethal
FT mutation)"
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
