NOP2_YEAST
ID NOP2_YEAST Reviewed; 618 AA.
AC P40991; D6W1B9; E9P914;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=25S rRNA (cytosine(2870)-C(5))-methyltransferase;
DE EC=2.1.1.310 {ECO:0000269|PubMed:23913415};
DE AltName: Full=Nucleolar protein 2;
GN Name=NOP2; Synonyms=YNA1; OrderedLocusNames=YNL061W;
GN ORFNames=N2428, YNL2428W;
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 [GENOMIC DNA].
RC STRAIN=BJ2168;
RX PubMed=7806561; DOI=10.1083/jcb.127.6.1799;
RA de Beus E., Brockenbrough J.S., Hong B., Aris J.P.;
RT "Yeast NOP2 encodes an essential nucleolar protein with homology to a human
RT proliferation marker.";
RL J. Cell Biol. 127:1799-1813(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=S288c / FY1676;
RX PubMed=8533472; DOI=10.1002/yea.320111008;
RA Bergez P., Doignon F., Crouzet M.;
RT "The sequence of a 44 420 bp fragment located on the left arm of chromosome
RT XIV from Saccharomyces cerevisiae.";
RL Yeast 11:967-974(1995).
RN [3]
RP ERRATUM OF PUBMED:8533472.
RX PubMed=8904343;
RX DOI=10.1002/(sici)1097-0061(19960315)12:3<297::aid-yea940>3.0.co;2-d;
RA Bergez P., Doignon F., Crouzet M.;
RL Yeast 12:297-297(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 146-618.
RC STRAIN=ATCC 204508 / S288c;
RA Garcia-Barrio M.T., Cuesta R., Hinnebusch A.G., Tamame Gonzalez M.;
RL Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP MUTAGENESIS OF CYS-424 AND CYS-478, AND FUNCTION.
RX PubMed=9854021; DOI=10.1042/bj3370029;
RA King M., Ton D., Redman K.L.;
RT "A conserved motif in the yeast nucleolar protein Nop2p contains an
RT essential cysteine residue.";
RL Biochem. J. 337:29-35(1999).
RN [9]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [10]
RP INTERACTION WITH NOP53, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15686447; DOI=10.1042/bj20041297;
RA Sydorskyy Y., Dilworth D.J., Halloran B., Yi E.C., Makhnevych T.,
RA Wozniak R.W., Aitchison J.D.;
RT "Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.";
RL Biochem. J. 388:819-826(2005).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-580, AND IDENTIFICATION BY
RP 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 [12]
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).
RN [13]
RP INTERACTION WITH TRM112.
RX PubMed=22956767; DOI=10.1091/mbc.e12-05-0370;
RA Sardana R., Johnson A.W.;
RT "The methyltransferase adaptor protein Trm112 is involved in biogenesis of
RT both ribosomal subunits.";
RL Mol. Biol. Cell 23:4313-4322(2012).
RN [14]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF CYS-424 AND CYS-478.
RX PubMed=23913415; DOI=10.1093/nar/gkt679;
RA Sharma S., Yang J., Watzinger P., Kotter P., Entian K.D.;
RT "Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA,
RT respectively.";
RL Nucleic Acids Res. 41:9062-9076(2013).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
CC specifically methylates the C(5) position of cytosine 2870 (m5C2870) in
CC 25S rRNA. Required for 60S ribosomal subunit synthesis and processing.
CC {ECO:0000269|PubMed:23913415, ECO:0000269|PubMed:9854021}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(2870) in 25S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(2870) in 25S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43176, Rhea:RHEA-COMP:10389, Rhea:RHEA-COMP:10390,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.310;
CC Evidence={ECO:0000269|PubMed:23913415};
CC -!- SUBUNIT: Interacts with NOP53. Interacts with TRM112.
CC {ECO:0000269|PubMed:15686447, ECO:0000269|PubMed:22956767}.
CC -!- INTERACTION:
CC P40991; Q02892: NOG1; NbExp=2; IntAct=EBI-12110, EBI-12105;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus.
CC -!- MISCELLANEOUS: Present with 18700 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|PROSITE-ProRule:PRU01023}.
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DR EMBL; X82656; CAA57979.1; -; Genomic_DNA.
DR EMBL; U12141; AAA99650.1; -; Genomic_DNA.
DR EMBL; Z71337; CAA95934.1; -; Genomic_DNA.
DR EMBL; AY693060; AAT93079.1; -; Genomic_DNA.
DR EMBL; X83512; CAA58502.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10485.1; -; Genomic_DNA.
DR PIR; A55188; A55188.
DR RefSeq; NP_014338.3; NM_001182899.3.
DR PDB; 6ELZ; EM; 3.30 A; q=1-618.
DR PDB; 6EM5; EM; 4.30 A; q=1-618.
DR PDB; 7OHR; EM; 4.72 A; q=1-618.
DR PDBsum; 6ELZ; -.
DR PDBsum; 6EM5; -.
DR PDBsum; 7OHR; -.
DR AlphaFoldDB; P40991; -.
DR SMR; P40991; -.
DR BioGRID; 35762; 813.
DR DIP; DIP-6488N; -.
DR IntAct; P40991; 82.
DR MINT; P40991; -.
DR STRING; 4932.YNL061W; -.
DR iPTMnet; P40991; -.
DR MaxQB; P40991; -.
DR PaxDb; P40991; -.
DR PRIDE; P40991; -.
DR DNASU; 855664; -.
DR EnsemblFungi; YNL061W_mRNA; YNL061W; YNL061W.
DR GeneID; 855664; -.
DR KEGG; sce:YNL061W; -.
DR SGD; S000005005; NOP2.
DR VEuPathDB; FungiDB:YNL061W; -.
DR eggNOG; KOG1122; Eukaryota.
DR GeneTree; ENSGT00940000161554; -.
DR HOGENOM; CLU_005316_3_2_1; -.
DR InParanoid; P40991; -.
DR OMA; FLAIPHM; -.
DR BioCyc; MetaCyc:G3O-33091-MON; -.
DR BioCyc; YEAST:G3O-33091-MON; -.
DR BRENDA; 2.1.1.310; 984.
DR PRO; PR:P40991; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P40991; protein.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0030687; C:preribosome, large subunit precursor; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IDA:SGD.
DR GO; GO:1902626; P:assembly of large subunit precursor of preribosome; IMP:SGD.
DR GO; GO:0000470; P:maturation of LSU-rRNA; IBA:GO_Central.
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:0042273; P:ribosomal large subunit biogenesis; IMP:SGD.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0070475; P:rRNA base methylation; IDA:SGD.
DR GO; GO:0031167; P:rRNA methylation; TAS:Reactome.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR031341; Methyltr_RsmF_N.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR011023; Nop2p.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR023273; RCMT_NOP2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR Pfam; PF17125; Methyltr_RsmF_N; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR PRINTS; PR02012; RCMTNOP2.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00446; nop2p; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..618
FT /note="25S rRNA (cytosine(2870)-C(5))-methyltransferase"
FT /id="PRO_0000211819"
FT REGION 1..132
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 18..50
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 76..90
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 91..132
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 478
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 353..359
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 377
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 404
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 421
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT MOD_RES 580
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950"
FT MUTAGEN 424
FT /note="C->A,S: Cannot complement loss of wild type NOP2."
FT /evidence="ECO:0000269|PubMed:23913415,
FT ECO:0000269|PubMed:9854021"
FT MUTAGEN 478
FT /note="C->A: Fails to ctalyze the C-5 methylation of the
FT C2870 residue and strongly affects 60S biogenesis."
FT /evidence="ECO:0000269|PubMed:23913415,
FT ECO:0000269|PubMed:9854021"
FT CONFLICT 216
FT /note="T -> A (in Ref. 6; AAT93079)"
FT /evidence="ECO:0000305"
FT CONFLICT 577
FT /note="I -> M (in Ref. 7; CAA58502)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 618 AA; 69812 MW; 6D11575703C6BB8B CRC64;
MGSRRHKNKQ AAPPTLEEFQ ARKEKKANRK LEKGKRPSTT QGDEVSDRKK KKSKPFKKSR
KEEEEVVEED KDLPEVDLEE LSKARKSLFD DEEDDDEAGL VDEELKDEFD LEQEYDYDED
EDNDAHPIFS DDDDEADLEE LNAQNMEALS KKLDEEEAEE AEEAEMELVE AENMQPRADI
LPTEEQEEMM AQETPNLTST RTRMIEIVKV LENFKTLGAE GRSRGEYVDR LLKDICEYFG
YTPFLAEKLF NLFSPAEAME FFEANEIARP ITIRTNTLKT RRRDLAQTLV NRGVNLQPIG
SWTKVGLQIF DSQVPIGATP EYLAGHYILQ AASSFLPVIA LDPHENERIL DMAAAPGGKT
TYISAMMKNT GCVFANDANK SRTKSLIANI HRLGCTNTIV CNYDAREFPK VIGGFDRILL
DAPCSGTGVI GKDQSVKVSR TEKDFIQIPH LQKQLLLSAI DSVDCNSKHG GVIVYSTCSV
AVEEDEAVID YALRKRPNVK LVDTGLAIGK EAFTSYRGKK FHPSVKLARR YYPHTYNVDG
FFVAKFQKIG PSSFDDNQAS AKEKETAARK EALEEGIIHS DFATFEDEED DKYIEKSVKN
NLLKKGVNPK AKRPSNEK
