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Protein

ATP-dependent rRNA helicase RRP3

Gene

RRP3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent rRNA helicase required for pre-ribosomal RNA processing. Involved in the maturation of the 35S-pre-rRNA and to its cleavage to mature 18S rRNA.4 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.3 Publications

Enzyme regulationi

ATPase activity is stimulated upon the addition of RNA.2 Publications

Kineticsi

  1. KM=2.3 mM for ATP1 Publication

    pH dependencei

    Optimum pH is 7.0-9.0.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi125 – 1328ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • ATP-dependent RNA helicase activity Source: SGD
    • RNA binding Source: UniProtKB-KW
    • RNA-dependent ATPase activity Source: SGD

    GO - Biological processi

    • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31116-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent rRNA helicase RRP3Curated (EC:3.6.4.133 Publications)
    Alternative name(s):
    Ribosomal RNA-processing protein 31 Publication
    Gene namesi
    Name:RRP31 Publication
    Ordered Locus Names:YHR065CImported
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome VIII

    Organism-specific databases

    EuPathDBiFungiDB:YHR065C.
    SGDiS000001107. RRP3.

    Subcellular locationi

    GO - Cellular componenti

    • nucleolus Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Leads to improper processing of 35S precursor rRNA.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi131 – 1311K → A or R: Leads to defects in A1 and A2 processing. 1 Publication
    Mutagenesisi231 – 2311D → A: Leads to defects in A1 and A2 processing. 1 Publication
    Mutagenesisi263 – 2631S → L: Leads to defects in A1 and A2 processing. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 501501ATP-dependent rRNA helicase RRP3PRO_0000055064Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei43 – 431PhosphoserineCombined sources
    Modified residuei45 – 451PhosphoserineCombined sources
    Modified residuei47 – 471PhosphoserineCombined sources

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38712.
    PeptideAtlasiP38712.

    PTM databases

    iPTMnetiP38712.

    Interactioni

    Subunit structurei

    Interacts with the SSU processome.1 Publication

    Protein-protein interaction databases

    BioGridi36497. 16 interactions.
    DIPiDIP-6533N.
    IntActiP38712. 2 interactions.
    MINTiMINT-518716.

    Structurei

    3D structure databases

    ProteinModelPortaliP38712.
    SMRiP38712. Positions 76-446.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini112 – 284173Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini307 – 461155Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili3 – 4442Sequence analysisAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi81 – 10929Q motifCuratedAdd
    BLAST
    Motifi231 – 2344DEAD boxCurated

    Domaini

    The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.Curated

    Sequence similaritiesi

    Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    GeneTreeiENSGT00730000110914.
    HOGENOMiHOG000268802.
    InParanoidiP38712.
    KOiK14777.
    OMAiKFKSKAR.
    OrthoDBiEOG7FR7R5.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR000629. RNA-helicase_DEAD-box_CS.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    [Graphical view]
    PfamiPF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
    PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P38712-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKIVKRKEK KANDELTSLA EKIRAKALEN QKKLIEAEKE GGSESDSEED
    60 70 80 90 100
    ATAEKKKVLK SKSKSTVSTQ NENTNEDESF ESFSELNLVP ELIQACKNLN
    110 120 130 140 150
    YSKPTPIQSK AIPPALEGHD IIGLAQTGSG KTAAFAIPIL NRLWHDQEPY
    160 170 180 190 200
    YACILAPTRE LAQQIKETFD SLGSLMGVRS TCIVGGMNMM DQARDLMRKP
    210 220 230 240 250
    HIIIATPGRL MDHLENTKGF SLRKLKFLVM DEADRLLDME FGPVLDRILK
    260 270 280 290 300
    IIPTQERTTY LFSATMTSKI DKLQRASLTN PVKCAVSNKY QTVDTLVQTL
    310 320 330 340 350
    MVVPGGLKNT YLIYLLNEFI GKTMIIFTRT KANAERLSGL CNLLEFSATA
    360 370 380 390 400
    LHGDLNQNQR MGSLDLFKAG KRSILVATDV AARGLDIPSV DIVVNYDIPV
    410 420 430 440 450
    DSKSYIHRVG RTARAGRSGK SISLVSQYDL ELILRIEEVL GKKLPKESVD
    460 470 480 490 500
    KNIILTLRDS VDKANGEVVM EMNRRNKEKI ARGKGRRGRM MTRENMDMGE

    R
    Length:501
    Mass (Da):55,969
    Last modified:November 8, 2005 - v2
    Checksum:iAA17798E0897272F
    GO

    Sequence cautioni

    The sequence AAB68392.1 differs from that shown. Reason: Erroneous initiation. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00061 Genomic DNA. Translation: AAB68392.1. Different initiation.
    AY389302 mRNA. Translation: AAQ97234.1.
    AY389303 mRNA. Translation: AAQ97235.1.
    BK006934 Genomic DNA. Translation: DAA06758.1.
    PIRiS46713.
    RefSeqiNP_011932.2. NM_001179195.1.

    Genome annotation databases

    EnsemblFungiiYHR065C; YHR065C; YHR065C.
    GeneIDi856462.
    KEGGisce:YHR065C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00061 Genomic DNA. Translation: AAB68392.1. Different initiation.
    AY389302 mRNA. Translation: AAQ97234.1.
    AY389303 mRNA. Translation: AAQ97235.1.
    BK006934 Genomic DNA. Translation: DAA06758.1.
    PIRiS46713.
    RefSeqiNP_011932.2. NM_001179195.1.

    3D structure databases

    ProteinModelPortaliP38712.
    SMRiP38712. Positions 76-446.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36497. 16 interactions.
    DIPiDIP-6533N.
    IntActiP38712. 2 interactions.
    MINTiMINT-518716.

    PTM databases

    iPTMnetiP38712.

    Proteomic databases

    MaxQBiP38712.
    PeptideAtlasiP38712.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYHR065C; YHR065C; YHR065C.
    GeneIDi856462.
    KEGGisce:YHR065C.

    Organism-specific databases

    EuPathDBiFungiDB:YHR065C.
    SGDiS000001107. RRP3.

    Phylogenomic databases

    GeneTreeiENSGT00730000110914.
    HOGENOMiHOG000268802.
    InParanoidiP38712.
    KOiK14777.
    OMAiKFKSKAR.
    OrthoDBiEOG7FR7R5.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31116-MONOMER.

    Miscellaneous databases

    NextBioi982111.
    PROiP38712.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR000629. RNA-helicase_DEAD-box_CS.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    [Graphical view]
    PfamiPF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
    PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Verification of 3' and 5' ends of S.cerevisiae transcripts."
      Kennedy M.C., Dietrich F.S.
      Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-72 AND 478-501.
      Strain: ATCC 204511 / S288c / AB972.
    4. "18S rRNA processing requires the RNA helicase-like protein Rrp3."
      O'Day C.L., Chavanikamannil F., Abelson J.
      Nucleic Acids Res. 24:3201-3207(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
    5. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
      Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
      Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
    6. "Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis."
      Granneman S., Bernstein K.A., Bleichert F., Baserga S.J.
      Mol. Cell. Biol. 26:1183-1194(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH THE SSU PROCESSOME, FUNCTION, MUTAGENESIS OF LYS-131; ASP-231 AND SER-263.
    7. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-43; SER-45 AND SER-47, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    8. "Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins."
      Garcia I., Uhlenbeck O.C.
      Biochemistry 47:12562-12573(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, RNA-BINDING.
    9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-43; SER-45 AND SER-47, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Duplex destabilization by four ribosomal DEAD-box proteins."
      Garcia I., Albring M.J., Uhlenbeck O.C.
      Biochemistry 51:10109-10118(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, RNA-BINDING.

    Entry informationi

    Entry nameiRRP3_YEAST
    AccessioniPrimary (citable) accession number: P38712
    Secondary accession number(s): D3DL14, Q6TQT5, Q6TQT6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 8, 2005
    Last modified: May 11, 2016
    This is version 140 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome VIII
      Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.