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 03-AUG-2022, entry version 181.
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; 151.
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-6533N; -.
DR IntAct; P38712; 7.
DR MINT; P38712; -.
DR STRING; 4932.YHR065C; -.
DR iPTMnet; P38712; -.
DR MaxQB; P38712; -.
DR PaxDb; P38712; -.
DR PRIDE; P38712; -.
DR EnsemblFungi; YHR065C_mRNA; YHR065C; YHR065C.
DR GeneID; 856462; -.
DR KEGG; sce:YHR065C; -.
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; YDIELYQ; -.
DR BioCyc; YEAST:G3O-31116-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
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; IC: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 Gene3D; 3.40.50.300; -; 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 Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 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
