ID   RCM1_YEAST              Reviewed;         490 AA.
AC   P53972; D6W1F7;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 1.
DT   27-MAR-2024, entry version 149.
DE   RecName: Full=25S rRNA (cytosine(2278)-C(5))-methyltransferase;
DE            EC=2.1.1.311 {ECO:0000269|PubMed:23913415, ECO:0000269|PubMed:25125595, ECO:0000269|PubMed:25635753};
DE   AltName: Full=rRNA m(5)C methyltransferase 1 {ECO:0000303|PubMed:23913415};
GN   Name=RCM1 {ECO:0000303|PubMed:23913415, ECO:0000312|SGD:S000004967};
GN   OrderedLocusNames=YNL022C; ORFNames=N2815;
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=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   [2]
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   [3]
RP   SUBCELLULAR LOCATION.
RX   PubMed=10649453;
RX   DOI=10.1002/(sici)1097-0061(200002)16:3<241::aid-yea517>3.0.co;2-t;
RA   Brachat A., Liebundguth N., Rebischung C., Lemire S., Schaerer F.,
RA   Hoepfner D., Demchyshyn V., Howald I., Duesterhoeft A., Moestl D.,
RA   Poehlmann R., Koetter P., Hall M.N., Wach A., Philippsen P.;
RT   "Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces
RT   cerevisiae open reading frames.";
RL   Yeast 16:241-253(2000).
RN   [4]
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   [5]
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   [6]
RP   FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP   CYS-330 AND CYS-404.
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).
RN   [7]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=25125595; DOI=10.1261/rna.043398.113;
RA   Gigova A., Duggimpudi S., Pollex T., Schaefer M., Kos M.;
RT   "A cluster of methylations in the domain IV of 25S rRNA is required for
RT   ribosome stability.";
RL   RNA 20:1632-1644(2014).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX   PubMed=25635753; DOI=10.1038/ncomms7158;
RA   Schosserer M., Minois N., Angerer T.B., Amring M., Dellago H.,
RA   Harreither E., Calle-Perez A., Pircher A., Gerstl M.P., Pfeifenberger S.,
RA   Brandl C., Sonntagbauer M., Kriegner A., Linder A., Weinhaeusel A.,
RA   Mohr T., Steiger M., Mattanovich D., Rinnerthaler M., Karl T., Sharma S.,
RA   Entian K.D., Kos M., Breitenbach M., Wilson I.B., Polacek N.,
RA   Grillari-Voglauer R., Breitenbach-Koller L., Grillari J.;
RT   "Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating
RT   organismal lifespan.";
RL   Nat. Commun. 6:6158-6158(2015).
CC   -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
CC       specifically methylates the C(5) position of cytosine 2278 (m5C2278) in
CC       25S rRNA (PubMed:23913415, PubMed:25125595, PubMed:25635753). Loss of
CC       m5C2278 in 25S rRNA results in anisomycin hypersensitivity
CC       (PubMed:23913415). {ECO:0000269|PubMed:23913415,
CC       ECO:0000269|PubMed:25125595, ECO:0000269|PubMed:25635753}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=cytidine(2278) in 25S rRNA + S-adenosyl-L-methionine = 5-
CC         methylcytidine(2278) in 25S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:43180, Rhea:RHEA-COMP:10391, Rhea:RHEA-COMP:10392,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.311;
CC         Evidence={ECO:0000269|PubMed:23913415, ECO:0000269|PubMed:25125595,
CC         ECO:0000269|PubMed:25635753};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:43181;
CC         Evidence={ECO:0000269|PubMed:23913415, ECO:0000269|PubMed:25125595,
CC         ECO:0000269|PubMed:25635753};
CC   -!- SUBUNIT: Interacts with TRM112. {ECO:0000269|PubMed:22956767}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:10649453,
CC       ECO:0000269|PubMed:23913415}.
CC   -!- DISRUPTION PHENOTYPE: Altered structural conformation of the ribosome
CC       in close proximity to cytosine 2278 (m5C2278) in 25S rRNA, leading to
CC       impaired translational fidelity, and promote recruitment of a distinct
CC       subset of oxidative stress-responsive mRNAs into polysomes.
CC       {ECO:0000269|PubMed:25635753}.
CC   -!- MISCELLANEOUS: Present with 922 molecules/cell in log phase SD medium.
CC       {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; Z71298; CAA95884.1; -; Genomic_DNA.
DR   EMBL; BK006947; DAA10523.1; -; Genomic_DNA.
DR   PIR; S62934; S62934.
DR   RefSeq; NP_014376.3; NM_001182861.3.
DR   AlphaFoldDB; P53972; -.
DR   SMR; P53972; -.
DR   BioGRID; 35804; 165.
DR   IntAct; P53972; 3.
DR   MINT; P53972; -.
DR   STRING; 4932.YNL022C; -.
DR   MaxQB; P53972; -.
DR   PaxDb; 4932-YNL022C; -.
DR   PeptideAtlas; P53972; -.
DR   EnsemblFungi; YNL022C_mRNA; YNL022C; YNL022C.
DR   GeneID; 855709; -.
DR   KEGG; sce:YNL022C; -.
DR   AGR; SGD:S000004967; -.
DR   SGD; S000004967; RCM1.
DR   VEuPathDB; FungiDB:YNL022C; -.
DR   eggNOG; KOG2360; Eukaryota.
DR   GeneTree; ENSGT00940000155974; -.
DR   HOGENOM; CLU_005316_7_4_1; -.
DR   InParanoid; P53972; -.
DR   OMA; SFKSRIY; -.
DR   OrthoDB; 102852at2759; -.
DR   BioCyc; MetaCyc:G3O-33060-MONOMER; -.
DR   BioCyc; YEAST:G3O-33060-MONOMER; -.
DR   BRENDA; 2.1.1.311; 984.
DR   BioGRID-ORCS; 855709; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P53972; -.
DR   Proteomes; UP000002311; Chromosome XIV.
DR   RNAct; P53972; Protein.
DR   GO; GO:0005730; C:nucleolus; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IDA:UniProtKB.
DR   GO; GO:0070475; P:rRNA base methylation; IDA:UniProtKB.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR   InterPro; IPR049560; MeTrfase_RsmB-F_NOP2_cat.
DR   InterPro; IPR001678; MeTrfase_RsmB-F_NOP2_dom.
DR   InterPro; IPR048889; NSUN5_RCM1_N.
DR   InterPro; IPR023267; RCMT.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   PANTHER; PTHR22807:SF4; 28S RRNA (CYTOSINE-C(5))-METHYLTRANSFERASE; 1.
DR   PANTHER; PTHR22807; NOP2 YEAST -RELATED NOL1/NOP2/FMU SUN DOMAIN-CONTAINING; 1.
DR   Pfam; PF01189; Methyltr_RsmB-F; 1.
DR   Pfam; PF21153; NSUN5_N; 1.
DR   PRINTS; PR02008; RCMTFAMILY.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE   1: Evidence at protein level;
KW   Methyltransferase; Nucleus; Reference proteome; RNA-binding;
KW   rRNA processing; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..490
FT                   /note="25S rRNA (cytosine(2278)-C(5))-methyltransferase"
FT                   /id="PRO_0000203461"
FT   ACT_SITE        404
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01023,
FT                   ECO:0000305|PubMed:23913415"
FT   BINDING         250..256
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT   BINDING         280
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT   BINDING         308
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT   BINDING         327
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT   MUTAGEN         330
FT                   /note="C->A: Lethal. Blocks the separation of the enzyme
FT                   from its RNA substrate."
FT                   /evidence="ECO:0000269|PubMed:23913415"
FT   MUTAGEN         404
FT                   /note="C->A: Fails to catalyze the C-5 methylation of the
FT                   C2278 residue."
FT                   /evidence="ECO:0000269|PubMed:23913415"
SQ   SEQUENCE   490 AA;  56177 MW;  BB90FF7944FEA4AD CRC64;
     MNFYRDATWV LEDIEKEAAK ERISGSMQTL VLKSCKRYKL KSNPKHIYAV LDSCWKYKPY
     LEKVMKKAHI LEDIPKKKGK PLFSRLTLLL LCHDLLLSKQ KRIQMGKHPI KDYVLKFKSP
     LHSEMVKLKL KLKVRELSEL VLSEDISNDL PPVRWIRINP LKCHPNGETE PVLAELRKKF
     TLKVDKWSEL VPGSIYYDEF IPNLFGIHPS DKITAHELYK HGKIIIQDRA SCFPAHILNP
     GPSDIVIDSC SAPGNKTTHT ASYIYPEPPK DNNTRIYAFE KDPERAKVLQ KMIKIAGCSP
     NISVNVGDFT KLATPEKYKD VTCFIVDPSC SGSGIFGRKF FDSFNRRKID DKDDDGGIVP
     DEQEEFIAKE ELQTRLAKLS SFQFQMVKHA MSFPAAKKIV YSTCSIHAEE NERVVIDLLL
     DKSVREWGWK VAPKREVIPS WPRRGKVEEF EEVFRDGVTY DPQQLAEGCI RALPKSDGGI
     GFFAVCFERD
//