RRP9_YEAST
ID RRP9_YEAST Reviewed; 573 AA.
AC Q06506; D6W4D3;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Ribosomal RNA-processing protein 9;
GN Name=RRP9; OrderedLocusNames=YPR137W;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
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 [3]
RP FUNCTION, AND ASSOCIATION WITH U3 SNORNA.
RX PubMed=11105764; DOI=10.1017/s1355838200001369;
RA Venema J., Vos H.R., Faber A.W., van Venrooij W.J., Raue H.A.;
RT "Yeast Rrp9p is an evolutionarily conserved U3 snoRNP protein essential for
RT early pre-rRNA processing cleavages and requires box C for its
RT association.";
RL RNA 6:1660-1671(2000).
RN [4]
RP IDENTIFICATION IN SSU PROCESSOME BY MASS SPECTROMETRY.
RX PubMed=12068309; DOI=10.1038/nature00769;
RA Dragon F., Gallagher J.E.G., Compagnone-Post P.A., Mitchell B.M.,
RA Porwancher K.A., Wehner K.A., Wormsley S., Settlage R.E., Shabanowitz J.,
RA Osheim Y., Beyer A.L., Hunt D.F., Baserga S.J.;
RT "A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA
RT biogenesis.";
RL Nature 417:967-970(2002).
RN [5]
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 [6]
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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, AND IDENTIFICATION BY
RP 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 [8]
RP INTERACTION WITH UTP25.
RX PubMed=20884785; DOI=10.1261/rna.2359810;
RA Charette J.M., Baserga S.J.;
RT "The DEAD-box RNA helicase-like Utp25 is an SSU processome component.";
RL RNA 16:2156-2169(2010).
RN [9]
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: Involved in nucleolar processing of pre-18S ribosomal RNA.
CC Required for efficient pre-rRNA cleavage at sites A0, A1 and A2, and
CC biosynthesis of 18S rRNA. {ECO:0000269|PubMed:11105764}.
CC -!- SUBUNIT: Interacts with UTP25. Component of the ribosomal small subunit
CC (SSU) processome composed of at least 40 protein subunits and snoRNA
CC U3. {ECO:0000269|PubMed:12068309, ECO:0000269|PubMed:20884785}.
CC -!- INTERACTION:
CC Q06506; P53254: UTP22; NbExp=4; IntAct=EBI-35124, EBI-1878;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- DOMAIN: The WD domains are required for nucleolar localization and U3
CC small nucleolar RNAs binding. {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 5130 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the WD repeat RRP9 family. {ECO:0000305}.
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DR EMBL; U40829; AAB68277.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11549.1; -; Genomic_DNA.
DR PIR; S69026; S69026.
DR RefSeq; NP_015463.1; NM_001184234.1.
DR PDB; 4J0X; X-ray; 2.50 A; A/B=127-573.
DR PDB; 5JPQ; EM; 7.30 A; Y=1-573.
DR PDB; 5TZS; EM; 5.10 A; g=1-573.
DR PDB; 5WLC; EM; 3.80 A; SG=1-573.
DR PDB; 5WYJ; EM; 8.70 A; 3F=1-573.
DR PDB; 5WYK; EM; 4.50 A; 3F=1-573.
DR PDB; 6KE6; EM; 3.40 A; 3F=1-573.
DR PDB; 6LQP; EM; 3.20 A; 3F=1-573.
DR PDB; 6LQQ; EM; 4.10 A; 3F=1-573.
DR PDB; 6LQR; EM; 8.60 A; 3F=1-573.
DR PDB; 6LQS; EM; 3.80 A; 3F=1-573.
DR PDB; 6LQT; EM; 4.90 A; 3F=1-572.
DR PDB; 6LQU; EM; 3.70 A; 3F=1-573.
DR PDB; 6LQV; EM; 4.80 A; 3F=1-573.
DR PDB; 6ND4; EM; 4.30 A; g=1-573.
DR PDB; 6ZQA; EM; 4.40 A; CH=1-573.
DR PDB; 6ZQB; EM; 3.90 A; CH=1-573.
DR PDB; 6ZQC; EM; 3.80 A; CH=1-573.
DR PDB; 6ZQD; EM; 3.80 A; CH=1-573.
DR PDB; 6ZQE; EM; 7.10 A; CH=1-573.
DR PDB; 7AJT; EM; 4.60 A; CH=1-573.
DR PDB; 7AJU; EM; 3.80 A; CH=1-573.
DR PDB; 7D4I; EM; 4.00 A; 3F=1-573.
DR PDB; 7D5S; EM; 4.60 A; 3F=1-573.
DR PDB; 7D5T; EM; 6.00 A; 3F=1-573.
DR PDB; 7D63; EM; 12.30 A; 3F=1-573.
DR PDBsum; 4J0X; -.
DR PDBsum; 5JPQ; -.
DR PDBsum; 5TZS; -.
DR PDBsum; 5WLC; -.
DR PDBsum; 5WYJ; -.
DR PDBsum; 5WYK; -.
DR PDBsum; 6KE6; -.
DR PDBsum; 6LQP; -.
DR PDBsum; 6LQQ; -.
DR PDBsum; 6LQR; -.
DR PDBsum; 6LQS; -.
DR PDBsum; 6LQT; -.
DR PDBsum; 6LQU; -.
DR PDBsum; 6LQV; -.
DR PDBsum; 6ND4; -.
DR PDBsum; 6ZQA; -.
DR PDBsum; 6ZQB; -.
DR PDBsum; 6ZQC; -.
DR PDBsum; 6ZQD; -.
DR PDBsum; 6ZQE; -.
DR PDBsum; 7AJT; -.
DR PDBsum; 7AJU; -.
DR PDBsum; 7D4I; -.
DR PDBsum; 7D5S; -.
DR PDBsum; 7D5T; -.
DR PDBsum; 7D63; -.
DR AlphaFoldDB; Q06506; -.
DR SMR; Q06506; -.
DR BioGRID; 36303; 98.
DR ComplexPortal; CPX-1604; Small ribosomal subunit processome, variant 1.
DR ComplexPortal; CPX-1607; Small ribosomal subunit processome, variant 2.
DR ComplexPortal; CPX-1608; Small ribosomal subunit processome, variant 3.
DR DIP; DIP-6537N; -.
DR IntAct; Q06506; 47.
DR MINT; Q06506; -.
DR STRING; 4932.YPR137W; -.
DR iPTMnet; Q06506; -.
DR MaxQB; Q06506; -.
DR PaxDb; Q06506; -.
DR PRIDE; Q06506; -.
DR EnsemblFungi; YPR137W_mRNA; YPR137W; YPR137W.
DR GeneID; 856255; -.
DR KEGG; sce:YPR137W; -.
DR SGD; S000006341; RRP9.
DR VEuPathDB; FungiDB:YPR137W; -.
DR eggNOG; KOG0299; Eukaryota.
DR GeneTree; ENSGT00940000158328; -.
DR HOGENOM; CLU_014017_1_0_1; -.
DR InParanoid; Q06506; -.
DR OMA; RIWKITE; -.
DR BioCyc; YEAST:G3O-34272-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:Q06506; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q06506; protein.
DR GO; GO:0030686; C:90S preribosome; HDA:SGD.
DR GO; GO:0031428; C:box C/D RNP complex; IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0032040; C:small-subunit processome; IDA:SGD.
DR GO; GO:0030515; F:snoRNA binding; IBA:GO_Central.
DR GO; GO:0034511; F:U3 snoRNA binding; IDA:SGD.
DR GO; GO:0000480; P:endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0000447; P:endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0000472; P:endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IC:ComplexPortal.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR039241; Rrp9-like.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR19865; PTHR19865; 1.
DR Pfam; PF00400; WD40; 1.
DR SMART; SM00320; WD40; 5.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 1.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Coiled coil; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Ribonucleoprotein; Ribosome biogenesis;
KW rRNA processing; WD repeat.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..573
FT /note="Ribosomal RNA-processing protein 9"
FT /id="PRO_0000269482"
FT REPEAT 234..273
FT /note="WD 1"
FT REPEAT 278..317
FT /note="WD 2"
FT REPEAT 320..359
FT /note="WD 3"
FT REPEAT 397..435
FT /note="WD 4"
FT REPEAT 471..509
FT /note="WD 5"
FT REPEAT 516..562
FT /note="WD 6"
FT REGION 1..63
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 32..106
FT /evidence="ECO:0000255"
FT COMPBIAS 1..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 29..55
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 50
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT TURN 137..139
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 141..151
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 157..163
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 194..200
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:4J0X"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 239..244
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 248..255
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 258..264
FT /evidence="ECO:0007829|PDB:4J0X"
FT TURN 265..268
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 269..275
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 283..288
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 292..299
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 302..308
FT /evidence="ECO:0007829|PDB:4J0X"
FT TURN 309..312
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 327..329
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 332..339
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 345..350
FT /evidence="ECO:0007829|PDB:4J0X"
FT TURN 351..354
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 355..360
FT /evidence="ECO:0007829|PDB:4J0X"
FT HELIX 365..372
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 402..409
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 412..417
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 422..426
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:4J0X"
FT TURN 437..440
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 477..480
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 484..490
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 492..494
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 496..501
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 508..514
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 519..528
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 537..546
FT /evidence="ECO:0007829|PDB:4J0X"
FT STRAND 562..569
FT /evidence="ECO:0007829|PDB:4J0X"
SQ SEQUENCE 573 AA; 65054 MW; 96BEAB7DC338E70E CRC64;
MSDVTQQKKR KRSKGEVNPS KPTVDEEITD PSSNEDEQLE VSDEEDALES EEEFEGENPA
DKRRRLAKQY LENLKSEAND ILTDNRNAEE KDLNNLKERT IDEYNNFDAG DLDKDIIASR
LKEDVAEQQG RVFRYFGDKL LISEAKQSFT RVGENNLTCI SCFQPVLNKY TFEESSNGDK
NKGRLFAYTV SKDLQLTKYD ITDFSKRPKK LKYAKGGAKY IPTSKHEYEN TTEGHYDEIL
TVAASPDGKY VVTGGRDRKL IVWSTESLSP VKVIPTKDRR GEVLSLAFRK NSDQLYASCA
DFKIRTYSIN QFSQLEILYG HHDIVEDISA LAMERCVTVG ARDRTAMLWK IPDETRLTFR
GGDEPQKLLR RWMKENAKEG EDGEVKYPDE SEAPLFFCEG SIDVVSMVDD FHFITGSDNG
NICLWSLAKK KPIFTERIAH GILPEPSFND ISGETDEELR KRQLQGKKLL QPFWITSLYA
IPYSNVFISG SWSGSLKVWK ISDNLRSFEL LGELSGAKGV VTKIQVVESG KHGKEKFRIL
ASIAKEHRLG RWIANVSGAR NGIYSAVIDQ TGF
