P25582 (SPB1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	841 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nucleolus Ref.6.
Sequence similarities	Belongs to the methyltransferase superfamily. RlmE family. SPB1 subfamily.

Ontologies

Keywords
Biological process	Ribosome biogenesis rRNA processing
Cellular component	Nucleus
Domain	Coiled coil
Ligand	S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5Ref.6. Source: SGD maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5Ref.6. Source: SGD
Cellular_component	nucleolus Inferred from direct assay Ref.5Ref.6. Source: SGD preribosome, large subunit precursor Inferred from direct assay PubMed 11583614. Source: SGD
Molecular_function	rRNA (guanine) methyltransferase activity Inferred from mutant phenotype Ref.9. Source: SGD rRNA (uridine-2'-O-)-methyltransferase activity Inferred from genetic interaction Ref.8. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 841	841	27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase HAMAP-Rule MF_03163		PRO_0000155604
Regions
	Coiled coil	360 – 389	30	Potential
	Compositional bias	704 – 841	138	Lys-rich HAMAP-Rule MF_03163
Sites
	Active site	159	1	Proton acceptor By similarity
	Binding site	58	1	S-adenosyl-L-methionine; via amide nitrogen By similarity
	Binding site	60	1	S-adenosyl-L-methionine; via amide nitrogen By similarity
	Binding site	78	1	S-adenosyl-L-methionine By similarity
	Binding site	94	1	S-adenosyl-L-methionine By similarity
	Binding site	119	1	S-adenosyl-L-methionine By similarity
Amino acid modifications
	Modified residue	455	1	Phosphoserine Ref.10
	Modified residue	529	1	Phosphoserine Ref.10 Ref.11 Ref.12
Experimental info
	Mutagenesis	52	1	D → A: Abolishes methyltransferase activity. Ref.8

Sequences

	Sequence		Length	Mass (Da)
	P25582 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: D7A080299B0C7E24	FASTA	841	96,485
	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

References

	« Hide 'large scale' referencesShow '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. , 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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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, 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, MASS SPECTROMETRY. Strain: ADR376.
[11]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-529, MASS SPECTROMETRY.
[12]	"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, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X59720 Genomic DNA. Translation: CAA42391.1. BK006937 Genomic DNA. Translation: DAA07432.1.
PIR	S74280.
RefSeq	NP_009877.1. NM_001178698.1.
3D structure databases
ProteinModelPortal	P25582.
SMR	P25582. Positions 25-202.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1777N.
IntAct	P25582. 9 interactions.
MINT	MINT-382661.
STRING	4932.YCL054W.
Proteomic databases
PaxDb	P25582.
PeptideAtlas	P25582.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YCL054W; YCL054W; YCL054W.
GeneID	850304.
KEGG	sce:YCL054W.
Organism-specific databases
CYGD	YCL054w.
SGD	S000000559. SPB1.
Phylogenomic databases
eggNOG	COG0293.
GeneTree	ENSGT00550000075004.
HOGENOM	HOG000176256.
KO	K14857.
OMA	REQMLDD.
OrthoDB	EOG4FN7SC.
Gene expression databases
Genevestigator	P25582.
GermOnline	YCL054W. Saccharomyces cerevisiae.
Family and domain databases
HAMAP	MF_01547. RNA_methyltr_E. MF_03163. RNA_methyltr_E_SPB1.
InterPro	IPR015507. rRNA-MeTfrase_E. IPR012920. rRNA_MeTfrase_Spb1_C. IPR024576. rRNA_MeTfrase_Spb1_DUF3381. IPR002877. rRNA_MeTrfase_FtsJ_dom. [Graphical view]
PANTHER	PTHR10920. PTHR10920. 1 hit.
Pfam	PF11861. DUF3381. 1 hit. PF01728. FtsJ. 1 hit. PF07780. Spb1_C. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	965688.

Entry information

Entry name

SPB1_YEAST

Accession

Primary (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:	May 1, 2013
This is version 115 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program