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P25582

- SPB1_YEAST

UniProt

P25582 - SPB1_YEAST

Protein

27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

Gene

SPB1

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 126 (01 Oct 2014)
      Sequence version 2 (30 May 2000)
      Previous versions | rss
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    Functioni

    Required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. Specifically methylates the guanosine in position 2922 of the 25S rRNA at the stage of 27S pre-rRNA maturation. Methylates also the uridine in position 2921 in the absence of methylation of this residue guided by snoRNA snR52 at the stage of 35S pre-rRNA maturation.3 PublicationsUniRule annotation

    Catalytic activityi

    S-adenosyl-L-methionine + guanosine(2922) in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(2922) in 27S pre-rRNA.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei58 – 581S-adenosyl-L-methionine; via amide nitrogenUniRule annotation
    Binding sitei60 – 601S-adenosyl-L-methionine; via amide nitrogenUniRule annotation
    Binding sitei78 – 781S-adenosyl-L-methionineUniRule annotation
    Binding sitei94 – 941S-adenosyl-L-methionineUniRule annotation
    Binding sitei119 – 1191S-adenosyl-L-methionineUniRule annotation
    Active sitei159 – 1591Proton acceptorUniRule annotation

    GO - Molecular functioni

    1. rRNA (guanine) methyltransferase activity Source: SGD
    2. rRNA (guanosine-2'-O-)-methyltransferase activity Source: UniProtKB-HAMAP
    3. rRNA (uridine-2'-O-)-methyltransferase activity Source: SGD

    GO - Biological processi

    1. enzyme-directed rRNA 2'-O-methylation Source: UniProtKB-HAMAP
    2. maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    3. maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    4. rRNA methylation Source: SGD

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciYEAST:YCL054W-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase (EC:2.1.1.167)
    Alternative name(s):
    2'-O-ribose RNA methyltransferase SPB1UniRule annotation
    AdoMet-dependent rRNA methyltransferase SPB1UniRule annotation
    S-adenosyl-L-methionine-dependent methyltransferaseUniRule annotation
    Suppressor of PAB1 protein 1
    Gene namesi
    Name:SPB1UniRule annotation
    Ordered Locus Names:YCL054W
    ORF Names:YCL431, YCL54W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome III

    Organism-specific databases

    CYGDiYCL054w.
    SGDiS000000559. SPB1.

    Subcellular locationi

    Nucleusnucleolus 1 PublicationUniRule annotation

    GO - Cellular componenti

    1. nucleolus Source: SGD
    2. nucleus Source: SGD
    3. preribosome, large subunit precursor Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi52 – 521D → A: Abolishes methyltransferase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 84184127S pre-rRNA (guanosine(2922)-2'-O)-methyltransferasePRO_0000155604Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei455 – 4551Phosphoserine2 Publications
    Modified residuei464 – 4641Phosphoserine1 Publication
    Modified residuei529 – 5291Phosphoserine3 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP25582.
    PaxDbiP25582.
    PeptideAtlasiP25582.

    Expressioni

    Gene expression databases

    GenevestigatoriP25582.

    Interactioni

    Subunit structurei

    Component of the nucleolar and nucleoplasmic pre-60S ribosomal particle. Interacts with the snoRNA-associated proteins NOP1 and NOP58.2 PublicationsUniRule annotation

    Protein-protein interaction databases

    BioGridi30932. 41 interactions.
    DIPiDIP-1777N.
    IntActiP25582. 8 interactions.
    MINTiMINT-8285150.
    STRINGi4932.YCL054W.

    Structurei

    3D structure databases

    ProteinModelPortaliP25582.
    SMRiP25582. Positions 25-202.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili360 – 38930UniRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi704 – 841138Lys-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the methyltransferase superfamily. RlmE family. SPB1 subfamily.UniRule annotation

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG0293.
    GeneTreeiENSGT00550000075004.
    HOGENOMiHOG000176256.
    KOiK14857.
    OMAiPRKKNGQ.
    OrthoDBiEOG7P02TJ.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    HAMAPiMF_01547. RNA_methyltr_E.
    MF_03163. RNA_methyltr_E_SPB1.
    InterProiIPR015507. rRNA-MeTfrase_E.
    IPR012920. rRNA_MeTfrase_Spb1_C.
    IPR024576. rRNA_MeTfrase_Spb1_DUF3381.
    IPR002877. rRNA_MeTrfase_FtsJ_dom.
    IPR029063. SAM-dependent_MTases-like.
    IPR028589. Spb1.
    [Graphical view]
    PANTHERiPTHR10920. PTHR10920. 1 hit.
    PTHR10920:SF13. PTHR10920:SF13. 1 hit.
    PfamiPF11861. DUF3381. 1 hit.
    PF01728. FtsJ. 1 hit.
    PF07780. Spb1_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P25582-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV    50
    IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVIT FQSDITTEDC 100
    RSKLRGYMKT WKADTVLHDG APNVGLGWVQ DAFTQSQLTL QALKLAVENL 150
    VVNGTFVTKI FRSKDYNKLI WVFQQLFEKV EATKPPASRN VSAEIFVVCK 200
    GFKAPKRLDP RLLDPKEVFE ELPDGQQNME SKIYNPEKKV RKRQGYEEGD 250
    NLLYHETSIL DFVRTEDPIS MLGEMNKFTI DENDHEWKIL KKLKQTTDEF 300
    RSCIEDLKVL GKKDFKMILR WRKIAREILG IEVKDDAKTE IEVVPLTEEE 350
    QIEKDLQGLQ EKQRLNVKRE RRRKNEMKQK ELQRMQMNMI TPTDIGIEAA 400
    SLGKESLFNL KTAEKTGILN DLAKGKKRMI FTDDELAKDN DIYIDENIMI 450
    KDKDSAADAD DLESELNAMY SDYKTRRSER DAKFRAKQAR GGDNEEEWTG 500
    FNEGSLEKKE EEGKDYIEDN DDEGVEGDSD DDEAITNLIS KLKGQEGDHK 550
    LSSKARMIFN DPIFNNVEPD LPVNTVNDGI MSSESVGDIS KLNKKRKHEE 600
    MHQKQDEADS SDESSSDDSD FEIVANDNAS EEFDSDYDSE EEKNQTKKEK 650
    HSRDIDIATV EAMTLAHQLA LGQKNKHDLV DEGFNRYTFR DTENLPDWFL 700
    EDEKEHSKIN KPITKEAAMA IKEKIKAMNA RPIKKVAEAK ARKRMRAVAR 750
    LEKIKKKAGL INDDSDKTEK DKAEEISRLM RKVTKKPKTK PKVTLVVASG 800
    RNKGLAGRPK GVKGKYKMVD GVMKNEQRAL RRIAKKHHKK K 841
    Length:841
    Mass (Da):96,485
    Last modified:May 30, 2000 - v2
    Checksum:iD7A080299B0C7E24
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X59720 Genomic DNA. Translation: CAA42391.1.
    BK006937 Genomic DNA. Translation: DAA07432.1.
    PIRiS74280.
    RefSeqiNP_009877.1. NM_001178698.1.

    Genome annotation databases

    EnsemblFungiiYCL054W; YCL054W; YCL054W.
    GeneIDi850304.
    KEGGisce:YCL054W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X59720 Genomic DNA. Translation: CAA42391.1 .
    BK006937 Genomic DNA. Translation: DAA07432.1 .
    PIRi S74280.
    RefSeqi NP_009877.1. NM_001178698.1.

    3D structure databases

    ProteinModelPortali P25582.
    SMRi P25582. Positions 25-202.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 30932. 41 interactions.
    DIPi DIP-1777N.
    IntActi P25582. 8 interactions.
    MINTi MINT-8285150.
    STRINGi 4932.YCL054W.

    Proteomic databases

    MaxQBi P25582.
    PaxDbi P25582.
    PeptideAtlasi P25582.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YCL054W ; YCL054W ; YCL054W .
    GeneIDi 850304.
    KEGGi sce:YCL054W.

    Organism-specific databases

    CYGDi YCL054w.
    SGDi S000000559. SPB1.

    Phylogenomic databases

    eggNOGi COG0293.
    GeneTreei ENSGT00550000075004.
    HOGENOMi HOG000176256.
    KOi K14857.
    OMAi PRKKNGQ.
    OrthoDBi EOG7P02TJ.

    Enzyme and pathway databases

    BioCyci YEAST:YCL054W-MONOMER.

    Miscellaneous databases

    NextBioi 965688.
    PROi P25582.

    Gene expression databases

    Genevestigatori P25582.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    HAMAPi MF_01547. RNA_methyltr_E.
    MF_03163. RNA_methyltr_E_SPB1.
    InterProi IPR015507. rRNA-MeTfrase_E.
    IPR012920. rRNA_MeTfrase_Spb1_C.
    IPR024576. rRNA_MeTfrase_Spb1_DUF3381.
    IPR002877. rRNA_MeTrfase_FtsJ_dom.
    IPR029063. SAM-dependent_MTases-like.
    IPR028589. Spb1.
    [Graphical view ]
    PANTHERi PTHR10920. PTHR10920. 1 hit.
    PTHR10920:SF13. PTHR10920:SF13. 1 hit.
    Pfami PF11861. DUF3381. 1 hit.
    PF01728. FtsJ. 1 hit.
    PF07780. Spb1_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53335. SSF53335. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The complete DNA sequence of yeast chromosome III."
      Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
      , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
      Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Gromadka R.
      Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO C-TERMINUS.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Nucleotide sequence of D10B, a BamHI fragment on the small-ring chromosome III of Saccharomyces cerevisiae."
      Defoor E., Debrabandere R., Keyers B., Voet M., Volckaert G.
      Yeast 8:681-687(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-214.
    5. "Spb1p is a putative methyltransferase required for 60S ribosomal subunit biogenesis in Saccharomyces cerevisiae."
      Kressler D., Rojo M., Linder P., de la Cruz J.
      Nucleic Acids Res. 27:4598-4608(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Spb1p is a yeast nucleolar protein associated with Nop1p and Nop58p that is able to bind S-adenosyl-L-methionine in vitro."
      Pintard L., Kressler D., Lapeyre B.
      Mol. Cell. Biol. 20:1370-1381(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: BINDING TO S-ADENOSYL-L-METHIONINE, INTERACTION WITH NOP1 AND NOP58, SUBCELLULAR LOCATION.
    7. "60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm."
      Nissan T.A., Bassler J., Petfalski E., Tollervey D., Hurt E.
      EMBO J. 21:5539-5547(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE PRE-60S RIBOSOMAL PARTICLE, IDENTIFICATION BY MASS SPECTROMETRY.
    8. "Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast."
      Bonnerot C., Pintard L., Lutfalla G.
      Mol. Cell 12:1309-1315(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-52.
    9. "Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage."
      Lapeyre B., Purushothaman S.K.
      Mol. Cell 16:663-669(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "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-455 AND SER-529, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    11. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-529, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "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-455; SER-464 AND SER-529, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiSPB1_YEAST
    AccessioniPrimary (citable) accession number: P25582
    Secondary accession number(s): D6VQW3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 30, 2000
    Last modified: October 1, 2014
    This is version 126 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 III
      Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

    External Data

    Dasty 3