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P25582

- SPB1_YEAST

UniProt

P25582 - SPB1_YEAST

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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

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
Complete GO annotation...

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
Complete GO annotation...

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 class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase 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

        10         20         30         40         50
MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV
60 70 80 90 100
IDLCAAPGSW CQVASKLCPV NSLIIGVDIV PMKPMPNVIT FQSDITTEDC
110 120 130 140 150
RSKLRGYMKT WKADTVLHDG APNVGLGWVQ DAFTQSQLTL QALKLAVENL
160 170 180 190 200
VVNGTFVTKI FRSKDYNKLI WVFQQLFEKV EATKPPASRN VSAEIFVVCK
210 220 230 240 250
GFKAPKRLDP RLLDPKEVFE ELPDGQQNME SKIYNPEKKV RKRQGYEEGD
260 270 280 290 300
NLLYHETSIL DFVRTEDPIS MLGEMNKFTI DENDHEWKIL KKLKQTTDEF
310 320 330 340 350
RSCIEDLKVL GKKDFKMILR WRKIAREILG IEVKDDAKTE IEVVPLTEEE
360 370 380 390 400
QIEKDLQGLQ EKQRLNVKRE RRRKNEMKQK ELQRMQMNMI TPTDIGIEAA
410 420 430 440 450
SLGKESLFNL KTAEKTGILN DLAKGKKRMI FTDDELAKDN DIYIDENIMI
460 470 480 490 500
KDKDSAADAD DLESELNAMY SDYKTRRSER DAKFRAKQAR GGDNEEEWTG
510 520 530 540 550
FNEGSLEKKE EEGKDYIEDN DDEGVEGDSD DDEAITNLIS KLKGQEGDHK
560 570 580 590 600
LSSKARMIFN DPIFNNVEPD LPVNTVNDGI MSSESVGDIS KLNKKRKHEE
610 620 630 640 650
MHQKQDEADS SDESSSDDSD FEIVANDNAS EEFDSDYDSE EEKNQTKKEK
660 670 680 690 700
HSRDIDIATV EAMTLAHQLA LGQKNKHDLV DEGFNRYTFR DTENLPDWFL
710 720 730 740 750
EDEKEHSKIN KPITKEAAMA IKEKIKAMNA RPIKKVAEAK ARKRMRAVAR
760 770 780 790 800
LEKIKKKAGL INDDSDKTEK DKAEEISRLM RKVTKKPKTK PKVTLVVASG
810 820 830 840
RNKGLAGRPK GVKGKYKMVD GVMKNEQRAL RRIAKKHHKK K
Length:841
Mass (Da):96,485
Last modified:May 30, 2000 - v2
Checksum:iD7A080299B0C7E24
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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

« Hide 'large scale' publications
  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 29, 2014
This is version 127 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