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P25582 (SPB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase

EC=2.1.1.167
Alternative name(s):
2'-O-ribose RNA methyltransferase SPB1
AdoMet-dependent rRNA methyltransferase SPB1
S-adenosyl-L-methionine-dependent methyltransferase
Suppressor of PAB1 protein 1
Gene names
Name:SPB1
Ordered Locus Names:YCL054W
ORF Names:YCL431, YCL54W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length841 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.8 Ref.9

Catalytic activity

S-adenosyl-L-methionine + guanosine(2922) in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(2922) in 27S pre-rRNA. Ref.8

Subunit structure

Component of the nucleolar and nucleoplasmic pre-60S ribosomal particle. Interacts with the snoRNA-associated proteins NOP1 and NOP58. Ref.6 Ref.7

Subcellular location

Nucleusnucleolus Ref.6.

Sequence similarities

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 84184127S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase HAMAP-Rule MF_03163
PRO_0000155604

Regions

Coiled coil360 – 38930 Potential
Compositional bias704 – 841138Lys-rich HAMAP-Rule MF_03163

Sites

Active site1591Proton acceptor By similarity
Binding site581S-adenosyl-L-methionine; via amide nitrogen By similarity
Binding site601S-adenosyl-L-methionine; via amide nitrogen By similarity
Binding site781S-adenosyl-L-methionine By similarity
Binding site941S-adenosyl-L-methionine By similarity
Binding site1191S-adenosyl-L-methionine By similarity

Amino acid modifications

Modified residue4551Phosphoserine Ref.10 Ref.12
Modified residue4641Phosphoserine Ref.12
Modified residue5291Phosphoserine Ref.10 Ref.11 Ref.12

Experimental info

Mutagenesis521D → A: Abolishes methyltransferase activity. Ref.8

Sequences

Sequence LengthMass (Da)Tools
P25582 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: D7A080299B0C7E24

FASTA84196,485
        10         20         30         40         50         60 
MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW 

        70         80         90        100        110        120 
CQVASKLCPV NSLIIGVDIV PMKPMPNVIT FQSDITTEDC RSKLRGYMKT WKADTVLHDG 

       130        140        150        160        170        180 
APNVGLGWVQ DAFTQSQLTL QALKLAVENL VVNGTFVTKI FRSKDYNKLI WVFQQLFEKV 

       190        200        210        220        230        240 
EATKPPASRN VSAEIFVVCK GFKAPKRLDP RLLDPKEVFE ELPDGQQNME SKIYNPEKKV 

       250        260        270        280        290        300 
RKRQGYEEGD NLLYHETSIL DFVRTEDPIS MLGEMNKFTI DENDHEWKIL KKLKQTTDEF 

       310        320        330        340        350        360 
RSCIEDLKVL GKKDFKMILR WRKIAREILG IEVKDDAKTE IEVVPLTEEE QIEKDLQGLQ 

       370        380        390        400        410        420 
EKQRLNVKRE RRRKNEMKQK ELQRMQMNMI TPTDIGIEAA SLGKESLFNL KTAEKTGILN 

       430        440        450        460        470        480 
DLAKGKKRMI FTDDELAKDN DIYIDENIMI KDKDSAADAD DLESELNAMY SDYKTRRSER 

       490        500        510        520        530        540 
DAKFRAKQAR GGDNEEEWTG FNEGSLEKKE EEGKDYIEDN DDEGVEGDSD DDEAITNLIS 

       550        560        570        580        590        600 
KLKGQEGDHK LSSKARMIFN DPIFNNVEPD LPVNTVNDGI MSSESVGDIS KLNKKRKHEE 

       610        620        630        640        650        660 
MHQKQDEADS SDESSSDDSD FEIVANDNAS EEFDSDYDSE EEKNQTKKEK HSRDIDIATV 

       670        680        690        700        710        720 
EAMTLAHQLA LGQKNKHDLV DEGFNRYTFR DTENLPDWFL EDEKEHSKIN KPITKEAAMA 

       730        740        750        760        770        780 
IKEKIKAMNA RPIKKVAEAK ARKRMRAVAR LEKIKKKAGL INDDSDKTEK DKAEEISRLM 

       790        800        810        820        830        840 
RKVTKKPKTK PKVTLVVASG RNKGLAGRPK GVKGKYKMVD GVMKNEQRAL RRIAKKHHKK 


K 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X59720 Genomic DNA. Translation: CAA42391.1.
BK006937 Genomic DNA. Translation: DAA07432.1.
PIRS74280.
RefSeqNP_009877.1. NM_001178698.1.

3D structure databases

ProteinModelPortalP25582.
SMRP25582. Positions 25-202.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid30932. 41 interactions.
DIPDIP-1777N.
IntActP25582. 8 interactions.
MINTMINT-8285150.
STRING4932.YCL054W.

Proteomic databases

MaxQBP25582.
PaxDbP25582.
PeptideAtlasP25582.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYCL054W; YCL054W; YCL054W.
GeneID850304.
KEGGsce:YCL054W.

Organism-specific databases

CYGDYCL054w.
SGDS000000559. SPB1.

Phylogenomic databases

eggNOGCOG0293.
GeneTreeENSGT00550000075004.
HOGENOMHOG000176256.
KOK14857.
OMAPRKKNGQ.
OrthoDBEOG7P02TJ.

Enzyme and pathway databases

BioCycYEAST:YCL054W-MONOMER.

Gene expression databases

GenevestigatorP25582.

Family and domain databases

Gene3D3.40.50.150. 1 hit.
HAMAPMF_01547. RNA_methyltr_E.
MF_03163. RNA_methyltr_E_SPB1.
InterProIPR015507. 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]
PANTHERPTHR10920. PTHR10920. 1 hit.
PTHR10920:SF13. PTHR10920:SF13. 1 hit.
PfamPF11861. DUF3381. 1 hit.
PF01728. FtsJ. 1 hit.
PF07780. Spb1_C. 1 hit.
[Graphical view]
SUPFAMSSF53335. SSF53335. 1 hit.
ProtoNetSearch...

Other

NextBio965688.
PROP25582.

Entry information

Entry nameSPB1_YEAST
AccessionPrimary (citable) accession number: P25582
Secondary accession number(s): D6VQW3
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 30, 2000
Last modified: June 11, 2014
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome III

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

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families