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P25808

- SPB4_YEAST

UniProt

P25808 - SPB4_YEAST

Protein

ATP-dependent rRNA helicase SPB4

Gene

SPB4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 1 (01 May 1992)
      Previous versions | rss
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    Functioni

    ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits. Required for the normal formation of 18S rRNA through the processing of pre-rRNAs at sites A0, A1 and A2, and the normal formation of 25S and 5.8S rRNAs through the processing of pre-rRNAs at sites C1 and C2.2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi51 – 588ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ATP-dependent RNA helicase activity Source: SGD
    3. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. assembly of large subunit precursor of preribosome Source: SGD
    2. ATP catabolic process Source: GOC
    3. maturation of LSU-rRNA Source: SGD
    4. ribosomal large subunit assembly Source: SGD

    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-30452-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ATP-dependent rRNA helicase SPB4 (EC:3.6.4.-)
    Alternative name(s):
    Suppressor of PAB1 protein 4
    Gene namesi
    Name:SPB4
    Ordered Locus Names:YFL002C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VI

    Organism-specific databases

    CYGDiYFL002c.
    SGDiS000001894. SPB4.

    Subcellular locationi

    Nucleusnucleolus 2 Publications

    GO - Cellular componenti

    1. 90S preribosome Source: SGD
    2. nucleolus Source: SGD
    3. nucleoplasm Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 606606ATP-dependent rRNA helicase SPB4PRO_0000055065Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei254 – 2541Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP25808.
    PaxDbiP25808.

    Expressioni

    Gene expression databases

    GenevestigatoriP25808.

    Interactioni

    Protein-protein interaction databases

    BioGridi31147. 377 interactions.
    DIPiDIP-5423N.
    IntActiP25808. 34 interactions.
    MINTiMINT-525740.
    STRINGi4932.YFL002C.

    Structurei

    3D structure databases

    ProteinModelPortaliP25808.
    SMRiP25808. Positions 18-429.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini38 – 224187Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini248 – 404157Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili539 – 58244Sequence AnalysisAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi7 – 3529Q motifAdd
    BLAST
    Motifi172 – 1754DEAD box

    Domaini

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

    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

    eggNOGiCOG0513.
    GeneTreeiENSGT00550000074969.
    HOGENOMiHOG000268803.
    KOiK14809.
    OMAiWDALTPP.
    OrthoDBiEOG7FR7R5.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR025313. DUF4217.
    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.
    PF13959. DUF4217. 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.

    P25808-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD    50
    SVTGSGKTAA FVIPVLEKVV KEEANTSKFK KAHFHSLIIA PTRELSRQIE 100
    SVVLSFLEHY PSDLFPIKCQ LLVGTNEATV RDDVSNFLRN RPQILIGTPG 150
    RVLDFLQMPA VKTSACSMVV MDEADRLLDM SFIKDTEKIL RLLPKQRRTG 200
    LFSATMRSAG SDIFKTGLRN PVRITVNSKN QAPSSLKLNY CVVNPAEKLQ 250
    LLVSILNNYK FKKCIVYFPT CVSVSYFYSF IQYLGKRNIL VNEVEIFSLH 300
    GKLQTSARTK TLTAFTDSLS NSVLFTTDVA ARGIDIPDVD LVIQLDPPTN 350
    TDMFMHRCGR TGRANRVGKA ITFLNEGREE DFIPFMQVKN VELEELDLEV 400
    KGITTNFYED FRNWILEDRD RFDKGVKAYV AFIKYYSNHS ATSIFRLQSL 450
    DYVGIAKLYG LFRLPRMPEI TKYLATEKQE GIFPGNWLVD PPVNMDEYKY 500
    KDKKREKERQ ETLKNISLIN DKKKLKSELK KKNLAWSDKT LTKERKLERK 550
    EKMSLKRKAI EEELKAEELD ENAEEERIKE DWKEIVLQNK RKKVSSKAIQ 600
    GNFDDL 606
    Length:606
    Mass (Da):69,422
    Last modified:May 1, 1992 - v1
    Checksum:iB2EC8B8B5E34AA10
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X16147 Genomic DNA. Translation: CAA34272.1.
    D50617 Genomic DNA. Translation: BAA09238.1.
    BK006940 Genomic DNA. Translation: DAA12439.1.
    PIRiS14942.
    RefSeqiNP_116654.1. NM_001179964.1.

    Genome annotation databases

    EnsemblFungiiYFL002C; YFL002C; YFL002C.
    GeneIDi850549.
    KEGGisce:YFL002C.

    Cross-referencesi

    Web resourcesi

    RNA helicases from the baker's yeast Saccharomyces cerevisiae

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X16147 Genomic DNA. Translation: CAA34272.1 .
    D50617 Genomic DNA. Translation: BAA09238.1 .
    BK006940 Genomic DNA. Translation: DAA12439.1 .
    PIRi S14942.
    RefSeqi NP_116654.1. NM_001179964.1.

    3D structure databases

    ProteinModelPortali P25808.
    SMRi P25808. Positions 18-429.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31147. 377 interactions.
    DIPi DIP-5423N.
    IntActi P25808. 34 interactions.
    MINTi MINT-525740.
    STRINGi 4932.YFL002C.

    Proteomic databases

    MaxQBi P25808.
    PaxDbi P25808.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YFL002C ; YFL002C ; YFL002C .
    GeneIDi 850549.
    KEGGi sce:YFL002C.

    Organism-specific databases

    CYGDi YFL002c.
    SGDi S000001894. SPB4.

    Phylogenomic databases

    eggNOGi COG0513.
    GeneTreei ENSGT00550000074969.
    HOGENOMi HOG000268803.
    KOi K14809.
    OMAi WDALTPP.
    OrthoDBi EOG7FR7R5.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30452-MONOMER.

    Miscellaneous databases

    NextBioi 966324.
    PROi P25808.

    Gene expression databases

    Genevestigatori P25808.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR025313. DUF4217.
    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 ]
    Pfami PF00270. DEAD. 1 hit.
    PF13959. DUF4217. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view ]
    SMARTi SM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    PROSITEi PS00039. DEAD_ATP_HELICASE. 1 hit.
    PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Translation initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46."
      Sachs A.B., Davis R.W.
      Science 247:1077-1079(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204511 / S288c / AB972.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "Spb4p, an essential putative RNA helicase, is required for a late step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae."
      de la Cruz J., Kressler D., Rojo M., Tollervey D., Linder P.
      RNA 4:1268-1281(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    8. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-254, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSPB4_YEAST
    AccessioniPrimary (citable) accession number: P25808
    Secondary accession number(s): D6VTM9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 1, 1992
    Last modified: October 1, 2014
    This is version 136 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 5740 molecules/cell in log phase SD medium.1 Publication

    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 VI
      Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

    External Data

    Dasty 3