SPB1_YEAST
ID SPB1_YEAST Reviewed; 841 AA.
AC P25582; D6VQW3;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase;
DE EC=2.1.1.167;
DE AltName: Full=2'-O-ribose RNA methyltransferase SPB1 {ECO:0000255|HAMAP-Rule:MF_03163};
DE AltName: Full=AdoMet-dependent rRNA methyltransferase SPB1 {ECO:0000255|HAMAP-Rule:MF_03163};
DE AltName: Full=S-adenosyl-L-methionine-dependent methyltransferase {ECO:0000255|HAMAP-Rule:MF_03163};
DE AltName: Full=Suppressor of PAB1 protein 1;
GN Name=SPB1 {ECO:0000255|HAMAP-Rule:MF_03163}; OrderedLocusNames=YCL054W;
GN ORFNames=YCL431, YCL54W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=1574125; DOI=10.1038/357038a0;
RA Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M.,
RA Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G.,
RA Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A.,
RA Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M., Carcano C.,
RA Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M.,
RA Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C.,
RA Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F.,
RA Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C.,
RA Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E.,
RA Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P.,
RA Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J.,
RA Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P.,
RA Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M.,
RA Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P.,
RA Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G.,
RA Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E.,
RA Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F.,
RA Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L.,
RA Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J.,
RA Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M.,
RA Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A.,
RA Richterich P., Roberts A.B., Rodriguez F., Sanz E.,
RA Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J.,
RA Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I.,
RA Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M.,
RA Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M.,
RA Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D.,
RA Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K.,
RA Sgouros J.G.;
RT "The complete DNA sequence of yeast chromosome III.";
RL Nature 357:38-46(1992).
RN [2]
RP SEQUENCE REVISION TO C-TERMINUS.
RA Gromadka R.;
RL Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-214.
RX PubMed=1441748; DOI=10.1002/yea.320080813;
RA Defoor E., Debrabandere R., Keyers B., Voet M., Volckaert G.;
RT "Nucleotide sequence of D10B, a BamHI fragment on the small-ring chromosome
RT III of Saccharomyces cerevisiae.";
RL Yeast 8:681-687(1992).
RN [5]
RP FUNCTION.
RX PubMed=10556316; DOI=10.1093/nar/27.23.4598;
RA Kressler D., Rojo M., Linder P., de la Cruz J.;
RT "Spb1p is a putative methyltransferase required for 60S ribosomal subunit
RT biogenesis in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 27:4598-4608(1999).
RN [6]
RP BINDING TO S-ADENOSYL-L-METHIONINE, INTERACTION WITH NOP1 AND NOP58, AND
RP SUBCELLULAR LOCATION.
RX PubMed=10648622; DOI=10.1128/mcb.20.4.1370-1381.2000;
RA Pintard L., Kressler D., Lapeyre B.;
RT "Spb1p is a yeast nucleolar protein associated with Nop1p and Nop58p that
RT is able to bind S-adenosyl-L-methionine in vitro.";
RL Mol. Cell. Biol. 20:1370-1381(2000).
RN [7]
RP IDENTIFICATION IN THE PRE-60S RIBOSOMAL PARTICLE, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=12374754; DOI=10.1093/emboj/cdf547;
RA Nissan T.A., Bassler J., Petfalski E., Tollervey D., Hurt E.;
RT "60S pre-ribosome formation viewed from assembly in the nucleolus until
RT export to the cytoplasm.";
RL EMBO J. 21:5539-5547(2002).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ASP-52.
RX PubMed=14636587; DOI=10.1016/s1097-2765(03)00435-0;
RA Bonnerot C., Pintard L., Lutfalla G.;
RT "Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-
RT O-ribose methylation of a conserved rRNA position in yeast.";
RL Mol. Cell 12:1309-1315(2003).
RN [9]
RP FUNCTION.
RX PubMed=15546625; DOI=10.1016/j.molcel.2004.10.022;
RA Lapeyre B., Purushothaman S.K.;
RT "Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs
RT at a late processing stage.";
RL Mol. Cell 16:663-669(2004).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-455 AND SER-529, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-529, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-455; SER-464 AND SER-529, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Required for proper assembly of pre-ribosomal particles
CC during the biogenesis of the 60S ribosomal subunit. Specifically
CC methylates the guanosine in position 2922 of the 25S rRNA at the stage
CC of 27S pre-rRNA maturation. Methylates also the uridine in position
CC 2921 in the absence of methylation of this residue guided by snoRNA
CC snR52 at the stage of 35S pre-rRNA maturation. {ECO:0000255|HAMAP-
CC Rule:MF_03163, ECO:0000269|PubMed:10556316,
CC ECO:0000269|PubMed:14636587, ECO:0000269|PubMed:15546625}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=guanosine(2922) in 27S pre-rRNA + S-adenosyl-L-methionine =
CC 2'-O-methylguanosine(2922) in 27S pre-rRNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42724, Rhea:RHEA-COMP:10200, Rhea:RHEA-
CC COMP:10201, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74269, ChEBI:CHEBI:74445; EC=2.1.1.167;
CC Evidence={ECO:0000269|PubMed:14636587};
CC -!- SUBUNIT: Component of the nucleolar and nucleoplasmic pre-60S ribosomal
CC particle. Interacts with the snoRNA-associated proteins NOP1 and NOP58.
CC {ECO:0000255|HAMAP-Rule:MF_03163, ECO:0000269|PubMed:10648622,
CC ECO:0000269|PubMed:12374754}.
CC -!- INTERACTION:
CC P25582; P43586: LOC1; NbExp=4; IntAct=EBI-17814, EBI-22906;
CC P25582; Q07896: NOC3; NbExp=3; IntAct=EBI-17814, EBI-36093;
CC P25582; Q12080: NOP53; NbExp=3; IntAct=EBI-17814, EBI-29395;
CC P25582; P36160: RPF2; NbExp=6; IntAct=EBI-17814, EBI-15881;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000255|HAMAP-
CC Rule:MF_03163, ECO:0000269|PubMed:10648622}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA methyltransferase RlmE family. SPB1 subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_03163}.
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DR EMBL; X59720; CAA42391.1; -; Genomic_DNA.
DR EMBL; BK006937; DAA07432.1; -; Genomic_DNA.
DR PIR; S74280; S74280.
DR RefSeq; NP_009877.1; NM_001178698.1.
DR PDB; 6ELZ; EM; 3.30 A; w=1-841.
DR PDB; 6EM5; EM; 4.30 A; w=1-841.
DR PDB; 6YLX; EM; 3.90 A; w=1-841.
DR PDB; 7OHR; EM; 4.72 A; w=1-841.
DR PDB; 7OHV; EM; 3.90 A; w=1-841.
DR PDBsum; 6ELZ; -.
DR PDBsum; 6EM5; -.
DR PDBsum; 6YLX; -.
DR PDBsum; 7OHR; -.
DR PDBsum; 7OHV; -.
DR AlphaFoldDB; P25582; -.
DR SMR; P25582; -.
DR BioGRID; 30932; 86.
DR DIP; DIP-1777N; -.
DR IntAct; P25582; 22.
DR MINT; P25582; -.
DR STRING; 4932.YCL054W; -.
DR iPTMnet; P25582; -.
DR MaxQB; P25582; -.
DR PaxDb; P25582; -.
DR PRIDE; P25582; -.
DR EnsemblFungi; YCL054W_mRNA; YCL054W; YCL054W.
DR GeneID; 850304; -.
DR KEGG; sce:YCL054W; -.
DR SGD; S000000559; SPB1.
DR VEuPathDB; FungiDB:YCL054W; -.
DR eggNOG; KOG1098; Eukaryota.
DR GeneTree; ENSGT00550000075004; -.
DR HOGENOM; CLU_009422_8_1_1; -.
DR OMA; LMWVFQQ; -.
DR BioCyc; YEAST:YCL054W-MON; -.
DR BRENDA; 2.1.1.167; 984.
DR PRO; PR:P25582; -.
DR Proteomes; UP000002311; Chromosome III.
DR RNAct; P25582; protein.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IDA:SGD.
DR GO; GO:0008173; F:RNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0016435; F:rRNA (guanine) methyltransferase activity; IMP:SGD.
DR GO; GO:0070039; F:rRNA (guanosine-2'-O-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008650; F:rRNA (uridine-2'-O-)-methyltransferase activity; IGI:SGD.
DR GO; GO:0000453; P:enzyme-directed rRNA 2'-O-methylation; IEA:UniProtKB-UniRule.
DR GO; GO:0000466; P:maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0031167; P:rRNA methylation; IDA:SGD.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01547; RNA_methyltr_E; 1.
DR HAMAP; MF_03163; RNA_methyltr_E_SPB1; 1.
DR InterPro; IPR002877; RNA_MeTrfase_FtsJ_dom.
DR InterPro; IPR015507; rRNA-MeTfrase_E.
DR InterPro; IPR012920; rRNA_MeTfrase_SPB1-like_C.
DR InterPro; IPR024576; rRNA_MeTfrase_Spb1_DUF3381.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR028589; SPB1-like.
DR Pfam; PF11861; DUF3381; 1.
DR Pfam; PF01728; FtsJ; 1.
DR Pfam; PF07780; Spb1_C; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Methyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; Ribosome biogenesis; rRNA processing;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..841
FT /note="27S pre-rRNA (guanosine(2922)-2'-O)-
FT methyltransferase"
FT /id="PRO_0000155604"
FT REGION 480..534
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 565..654
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 360..389
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT COMPBIAS 480..515
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 516..533
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 570..588
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 589..610
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 611..639
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 640..654
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 159
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT BINDING 58
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT BINDING 60
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT BINDING 78
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT BINDING 94
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT BINDING 119
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03163"
FT MOD_RES 455
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 464
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 529
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MUTAGEN 52
FT /note="D->A: Abolishes methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:14636587"
SQ SEQUENCE 841 AA; 96485 MW; D7A080299B0C7E24 CRC64;
MGKTQKKNSK GRLDRYYYLA KEKGYRARSS FKIIQINEKY GHFLEKSKVV IDLCAAPGSW
CQVASKLCPV NSLIIGVDIV PMKPMPNVIT FQSDITTEDC RSKLRGYMKT WKADTVLHDG
APNVGLGWVQ DAFTQSQLTL QALKLAVENL VVNGTFVTKI FRSKDYNKLI WVFQQLFEKV
EATKPPASRN VSAEIFVVCK GFKAPKRLDP RLLDPKEVFE ELPDGQQNME SKIYNPEKKV
RKRQGYEEGD NLLYHETSIL DFVRTEDPIS MLGEMNKFTI DENDHEWKIL KKLKQTTDEF
RSCIEDLKVL GKKDFKMILR WRKIAREILG IEVKDDAKTE IEVVPLTEEE QIEKDLQGLQ
EKQRLNVKRE RRRKNEMKQK ELQRMQMNMI TPTDIGIEAA SLGKESLFNL KTAEKTGILN
DLAKGKKRMI FTDDELAKDN DIYIDENIMI KDKDSAADAD DLESELNAMY SDYKTRRSER
DAKFRAKQAR GGDNEEEWTG FNEGSLEKKE EEGKDYIEDN DDEGVEGDSD DDEAITNLIS
KLKGQEGDHK LSSKARMIFN DPIFNNVEPD LPVNTVNDGI MSSESVGDIS KLNKKRKHEE
MHQKQDEADS SDESSSDDSD FEIVANDNAS EEFDSDYDSE EEKNQTKKEK HSRDIDIATV
EAMTLAHQLA LGQKNKHDLV DEGFNRYTFR DTENLPDWFL EDEKEHSKIN KPITKEAAMA
IKEKIKAMNA RPIKKVAEAK ARKRMRAVAR LEKIKKKAGL INDDSDKTEK DKAEEISRLM
RKVTKKPKTK PKVTLVVASG RNKGLAGRPK GVKGKYKMVD GVMKNEQRAL RRIAKKHHKK
K
