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P53972

- RCM1_YEAST

UniProt

P53972 - RCM1_YEAST

Protein

25S rRNA (cytosine(2278)-C(5))-methyltransferase

Gene

RCM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the C5 position of cytosine 2278 (m5C2278) in 25S rRNA. Loss of m5C2278 in 25S rRNA results in anisomycin hypersensitivity.1 Publication

    Catalytic activityi

    S-adenosyl-L-methionine + cytosine(2278) in 25S rRNA = S-adenosyl-L-homocysteine + C(5)-methylcytosine(2278) in 25S rRNA.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei280 – 2801S-adenosyl-L-methioninePROSITE-ProRule annotation
    Binding sitei308 – 3081S-adenosyl-L-methioninePROSITE-ProRule annotation
    Binding sitei327 – 3271S-adenosyl-L-methioninePROSITE-ProRule annotation
    Active sitei404 – 4041NucleophilePROSITE-ProRule annotation

    GO - Molecular functioni

    1. RNA binding Source: UniProtKB-KW
    2. rRNA (cytosine-C5-)-methyltransferase activity Source: SGD

    GO - Biological processi

    1. rRNA base methylation Source: SGD

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33060-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    25S rRNA (cytosine(2278)-C(5))-methyltransferase (EC:2.1.1.-)
    Alternative name(s):
    rRNA m(5)C methyltransferase 1
    Gene namesi
    Name:RCM1
    Ordered Locus Names:YNL022C
    ORF Names:N2815
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIV

    Organism-specific databases

    CYGDiYNL022c.
    SGDiS000004967. RCM1.

    Subcellular locationi

    Nucleusnucleolus 2 Publications

    GO - Cellular componenti

    1. nucleolus Source: SGD
    2. nucleus Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi330 – 3301C → A: Lethal. Blocks the separation of the enzyme from its RNA substrate. 1 Publication
    Mutagenesisi404 – 4041C → A: Fails to ctalyze the C-5 methylation of the C2278 residue. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 49049025S rRNA (cytosine(2278)-C(5))-methyltransferasePRO_0000203461Add
    BLAST

    Proteomic databases

    MaxQBiP53972.
    PaxDbiP53972.
    PeptideAtlasiP53972.

    Expressioni

    Gene expression databases

    GenevestigatoriP53972.

    Interactioni

    Subunit structurei

    Interacts with TRM112.1 Publication

    Protein-protein interaction databases

    BioGridi35804. 43 interactions.
    IntActiP53972. 1 interaction.
    MINTiMINT-2491929.
    STRINGi4932.YNL022C.

    Structurei

    3D structure databases

    ProteinModelPortaliP53972.
    SMRiP53972. Positions 154-489.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni250 – 2567S-adenosyl-L-methionine bindingPROSITE-ProRule annotation

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0144.
    GeneTreeiENSGT00550000074709.
    HOGENOMiHOG000203203.
    KOiK15264.
    OMAiRCSPGED.
    OrthoDBiEOG74R21C.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR001678. Fmu/NOL1/Nop2p.
    IPR023267. RCMT.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PfamiPF01189. Nol1_Nop2_Fmu. 1 hit.
    [Graphical view]
    PRINTSiPR02008. RCMTFAMILY.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    PROSITEiPS51686. SAM_MT_RSMB_NOP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P53972-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNFYRDATWV LEDIEKEAAK ERISGSMQTL VLKSCKRYKL KSNPKHIYAV    50
    LDSCWKYKPY LEKVMKKAHI LEDIPKKKGK PLFSRLTLLL LCHDLLLSKQ 100
    KRIQMGKHPI KDYVLKFKSP LHSEMVKLKL KLKVRELSEL VLSEDISNDL 150
    PPVRWIRINP LKCHPNGETE PVLAELRKKF TLKVDKWSEL VPGSIYYDEF 200
    IPNLFGIHPS DKITAHELYK HGKIIIQDRA SCFPAHILNP GPSDIVIDSC 250
    SAPGNKTTHT ASYIYPEPPK DNNTRIYAFE KDPERAKVLQ KMIKIAGCSP 300
    NISVNVGDFT KLATPEKYKD VTCFIVDPSC SGSGIFGRKF FDSFNRRKID 350
    DKDDDGGIVP DEQEEFIAKE ELQTRLAKLS SFQFQMVKHA MSFPAAKKIV 400
    YSTCSIHAEE NERVVIDLLL DKSVREWGWK VAPKREVIPS WPRRGKVEEF 450
    EEVFRDGVTY DPQQLAEGCI RALPKSDGGI GFFAVCFERD 490
    Length:490
    Mass (Da):56,177
    Last modified:October 1, 1996 - v1
    Checksum:iBB90FF7944FEA4AD
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z71298 Genomic DNA. Translation: CAA95884.1.
    BK006947 Genomic DNA. Translation: DAA10523.1.
    PIRiS62934.
    RefSeqiNP_014376.3. NM_001182861.3.

    Genome annotation databases

    EnsemblFungiiYNL022C; YNL022C; YNL022C.
    GeneIDi855709.
    KEGGisce:YNL022C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z71298 Genomic DNA. Translation: CAA95884.1 .
    BK006947 Genomic DNA. Translation: DAA10523.1 .
    PIRi S62934.
    RefSeqi NP_014376.3. NM_001182861.3.

    3D structure databases

    ProteinModelPortali P53972.
    SMRi P53972. Positions 154-489.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35804. 43 interactions.
    IntActi P53972. 1 interaction.
    MINTi MINT-2491929.
    STRINGi 4932.YNL022C.

    Proteomic databases

    MaxQBi P53972.
    PaxDbi P53972.
    PeptideAtlasi P53972.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YNL022C ; YNL022C ; YNL022C .
    GeneIDi 855709.
    KEGGi sce:YNL022C.

    Organism-specific databases

    CYGDi YNL022c.
    SGDi S000004967. RCM1.

    Phylogenomic databases

    eggNOGi COG0144.
    GeneTreei ENSGT00550000074709.
    HOGENOMi HOG000203203.
    KOi K15264.
    OMAi RCSPGED.
    OrthoDBi EOG74R21C.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33060-MONOMER.

    Miscellaneous databases

    NextBioi 980055.
    PROi P53972.

    Gene expression databases

    Genevestigatori P53972.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    InterProi IPR001678. Fmu/NOL1/Nop2p.
    IPR023267. RCMT.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    Pfami PF01189. Nol1_Nop2_Fmu. 1 hit.
    [Graphical view ]
    PRINTSi PR02008. RCMTFAMILY.
    SUPFAMi SSF53335. SSF53335. 1 hit.
    PROSITEi PS51686. SAM_MT_RSMB_NOP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
      Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
      , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
      Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames."
      Brachat A., Liebundguth N., Rebischung C., Lemire S., Schaerer F., Hoepfner D., Demchyshyn V., Howald I., Duesterhoeft A., Moestl D., Poehlmann R., Koetter P., Hall M.N., Wach A., Philippsen P.
      Yeast 16:241-253(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    5. "The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits."
      Sardana R., Johnson A.W.
      Mol. Biol. Cell 23:4313-4322(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TRM112.
    6. "Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively."
      Sharma S., Yang J., Watzinger P., Kotter P., Entian K.D.
      Nucleic Acids Res. 41:9062-9076(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-330 AND CYS-404.

    Entry informationi

    Entry nameiRCM1_YEAST
    AccessioniPrimary (citable) accession number: P53972
    Secondary accession number(s): D6W1F7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 94 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 922 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome XIV
      Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

    External Data

    Dasty 3