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Entry: RRP3_YEAST
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Original site: RRP3_YEAST 
ID   RRP3_YEAST              Reviewed;         501 AA.
AC   P38712; D3DL14; Q6TQT5; Q6TQT6;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   08-NOV-2005, sequence version 2.
DT   08-NOV-2023, entry version 186.
DE   RecName: Full=ATP-dependent rRNA helicase RRP3 {ECO:0000305};
DE            EC=3.6.4.13 {ECO:0000269|PubMed:18975973, ECO:0000269|PubMed:23153376, ECO:0000269|PubMed:8774901};
DE   AltName: Full=Ribosomal RNA-processing protein 3 {ECO:0000303|PubMed:8774901};
GN   Name=RRP3 {ECO:0000303|PubMed:8774901};
GN   OrderedLocusNames=YHR065C {ECO:0000312|SGD:S000001107};
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=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   [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   NUCLEOTIDE SEQUENCE [MRNA] OF 1-72 AND 478-501.
RC   STRAIN=ATCC 204511 / S288c / AB972;
RA   Kennedy M.C., Dietrich F.S.;
RT   "Verification of 3' and 5' ends of S.cerevisiae transcripts.";
RL   Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX   PubMed=8774901; DOI=10.1093/nar/24.16.3201;
RA   O'Day C.L., Chavanikamannil F., Abelson J.;
RT   "18S rRNA processing requires the RNA helicase-like protein Rrp3.";
RL   Nucleic Acids Res. 24:3201-3207(1996).
RN   [5]
RP   IDENTIFICATION OF PROBABLE INITIATION SITE.
RX   PubMed=12748633; DOI=10.1038/nature01644;
RA   Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT   "Sequencing and comparison of yeast species to identify genes and
RT   regulatory elements.";
RL   Nature 423:241-254(2003).
RN   [6]
RP   INTERACTION WITH THE SSU PROCESSOME, FUNCTION, AND MUTAGENESIS OF LYS-131;
RP   ASP-231 AND SER-263.
RX   PubMed=16449634; DOI=10.1128/mcb.26.4.1183-1194.2006;
RA   Granneman S., Bernstein K.A., Bleichert F., Baserga S.J.;
RT   "Comprehensive mutational analysis of yeast DEXD/H box RNA helicases
RT   required for small ribosomal subunit synthesis.";
RL   Mol. Cell. Biol. 26:1183-1194(2006).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-43; SER-45 AND SER-47, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP   REGULATION, AND RNA-BINDING.
RX   PubMed=18975973; DOI=10.1021/bi8016119;
RA   Garcia I., Uhlenbeck O.C.;
RT   "Differential RNA-dependent ATPase activities of four rRNA processing yeast
RT   DEAD-box proteins.";
RL   Biochemistry 47:12562-12573(2008).
RN   [9]
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   [10]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-43; SER-45 AND SER-47, AND
RP   IDENTIFICATION BY 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   [11]
RP   FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND RNA-BINDING.
RX   PubMed=23153376; DOI=10.1021/bi301172s;
RA   Garcia I., Albring M.J., Uhlenbeck O.C.;
RT   "Duplex destabilization by four ribosomal DEAD-box proteins.";
RL   Biochemistry 51:10109-10118(2012).
CC   -!- FUNCTION: ATP-dependent rRNA helicase required for pre-ribosomal RNA
CC       processing. Involved in the maturation of the 35S-pre-rRNA and to its
CC       cleavage to mature 18S rRNA. {ECO:0000269|PubMed:16449634,
CC       ECO:0000269|PubMed:18975973, ECO:0000269|PubMed:23153376,
CC       ECO:0000269|PubMed:8774901}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC         Evidence={ECO:0000269|PubMed:18975973, ECO:0000269|PubMed:23153376,
CC         ECO:0000269|PubMed:8774901};
CC   -!- ACTIVITY REGULATION: ATPase activity is stimulated upon the addition of
CC       RNA. {ECO:0000269|PubMed:18975973, ECO:0000269|PubMed:23153376}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=2.3 mM for ATP {ECO:0000269|PubMed:18975973};
CC       pH dependence:
CC         Optimum pH is 7.0-9.0. {ECO:0000269|PubMed:18975973};
CC   -!- SUBUNIT: Interacts with the SSU processome.
CC       {ECO:0000269|PubMed:16449634}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC   -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC       family of RNA helicases and controls ATP binding and hydrolysis.
CC       {ECO:0000305}.
CC   -!- DISRUPTION PHENOTYPE: Leads to improper processing of 35S precursor
CC       rRNA. {ECO:0000269|PubMed:8774901}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX47/RRP3
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAB68392.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; U00061; AAB68392.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AY389302; AAQ97234.1; -; mRNA.
DR   EMBL; AY389303; AAQ97235.1; -; mRNA.
DR   EMBL; BK006934; DAA06758.1; -; Genomic_DNA.
DR   PIR; S46713; S46713.
DR   RefSeq; NP_011932.2; NM_001179195.1.
DR   AlphaFoldDB; P38712; -.
DR   SMR; P38712; -.
DR   BioGRID; 36497; 154.
DR   DIP; DIP-6533N; -.
DR   IntAct; P38712; 7.
DR   MINT; P38712; -.
DR   STRING; 4932.YHR065C; -.
DR   iPTMnet; P38712; -.
DR   MaxQB; P38712; -.
DR   PaxDb; 4932-YHR065C; -.
DR   PeptideAtlas; P38712; -.
DR   EnsemblFungi; YHR065C_mRNA; YHR065C; YHR065C.
DR   GeneID; 856462; -.
DR   KEGG; sce:YHR065C; -.
DR   AGR; SGD:S000001107; -.
DR   SGD; S000001107; RRP3.
DR   VEuPathDB; FungiDB:YHR065C; -.
DR   eggNOG; KOG0330; Eukaryota.
DR   GeneTree; ENSGT00940000155774; -.
DR   HOGENOM; CLU_003041_1_1_1; -.
DR   InParanoid; P38712; -.
DR   OMA; IAAETRW; -.
DR   OrthoDB; 149428at2759; -.
DR   BioCyc; YEAST:G3O-31116-MONOMER; -.
DR   Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR   BioGRID-ORCS; 856462; 5 hits in 10 CRISPR screens.
DR   PRO; PR:P38712; -.
DR   Proteomes; UP000002311; Chromosome VIII.
DR   RNAct; P38712; Protein.
DR   GO; GO:0005730; C:nucleolus; IDA:ComplexPortal.
DR   GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0032040; C:small-subunit processome; IPI:ComplexPortal.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR   GO; GO:0008186; F:ATP-dependent activity, acting on RNA; IDA:SGD.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003724; F:RNA helicase activity; IDA:SGD.
DR   GO; GO:0030490; P:maturation of SSU-rRNA; NAS:ComplexPortal.
DR   GO; GO:0000462; P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR   GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR   CDD; cd17954; DEADc_DDX47; 1.
DR   CDD; cd18787; SF2_C_DEAD; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
DR   InterPro; IPR044765; DDX47/Rrp3_DEADc.
DR   InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR   InterPro; IPR014001; Helicase_ATP-bd.
DR   InterPro; IPR001650; Helicase_C.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR   InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR   PANTHER; PTHR47959:SF1; ATP-DEPENDENT RNA HELICASE DBPA; 1.
DR   PANTHER; PTHR47959; ATP-DEPENDENT RNA HELICASE RHLE-RELATED; 1.
DR   Pfam; PF00270; DEAD; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR   PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR   PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR   PROSITE; PS51194; HELICASE_CTER; 1.
DR   PROSITE; PS51195; Q_MOTIF; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Coiled coil; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW   Phosphoprotein; Reference proteome; Ribosome biogenesis; RNA-binding;
KW   rRNA processing.
FT   CHAIN           1..501
FT                   /note="ATP-dependent rRNA helicase RRP3"
FT                   /id="PRO_0000055064"
FT   DOMAIN          112..284
FT                   /note="Helicase ATP-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   DOMAIN          307..461
FT                   /note="Helicase C-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT   REGION          36..79
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          480..501
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          3..44
FT                   /evidence="ECO:0000255"
FT   MOTIF           81..109
FT                   /note="Q motif"
FT                   /evidence="ECO:0000305"
FT   MOTIF           231..234
FT                   /note="DEAD box"
FT                   /evidence="ECO:0000305"
FT   COMPBIAS        36..61
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        63..79
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        485..501
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         125..132
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT   MOD_RES         43
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         45
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         47
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MUTAGEN         131
FT                   /note="K->A,R: Leads to defects in A1 and A2 processing."
FT                   /evidence="ECO:0000269|PubMed:16449634"
FT   MUTAGEN         231
FT                   /note="D->A: Leads to defects in A1 and A2 processing."
FT                   /evidence="ECO:0000269|PubMed:16449634"
FT   MUTAGEN         263
FT                   /note="S->L: Leads to defects in A1 and A2 processing."
FT                   /evidence="ECO:0000269|PubMed:16449634"
SQ   SEQUENCE   501 AA;  55969 MW;  AA17798E0897272F CRC64;
     MSKIVKRKEK KANDELTSLA EKIRAKALEN QKKLIEAEKE GGSESDSEED ATAEKKKVLK
     SKSKSTVSTQ NENTNEDESF ESFSELNLVP ELIQACKNLN YSKPTPIQSK AIPPALEGHD
     IIGLAQTGSG KTAAFAIPIL NRLWHDQEPY YACILAPTRE LAQQIKETFD SLGSLMGVRS
     TCIVGGMNMM DQARDLMRKP HIIIATPGRL MDHLENTKGF SLRKLKFLVM DEADRLLDME
     FGPVLDRILK IIPTQERTTY LFSATMTSKI DKLQRASLTN PVKCAVSNKY QTVDTLVQTL
     MVVPGGLKNT YLIYLLNEFI GKTMIIFTRT KANAERLSGL CNLLEFSATA LHGDLNQNQR
     MGSLDLFKAG KRSILVATDV AARGLDIPSV DIVVNYDIPV DSKSYIHRVG RTARAGRSGK
     SISLVSQYDL ELILRIEEVL GKKLPKESVD KNIILTLRDS VDKANGEVVM EMNRRNKEKI
     ARGKGRRGRM MTRENMDMGE R
//
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