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P53972

- RCM1_YEAST

UniProt

P53972 - RCM1_YEAST

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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

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
Complete GO annotation...

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
Complete GO annotation...

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. 44 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.
InParanoidiP53972.
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

        10         20         30         40         50
MNFYRDATWV LEDIEKEAAK ERISGSMQTL VLKSCKRYKL KSNPKHIYAV
60 70 80 90 100
LDSCWKYKPY LEKVMKKAHI LEDIPKKKGK PLFSRLTLLL LCHDLLLSKQ
110 120 130 140 150
KRIQMGKHPI KDYVLKFKSP LHSEMVKLKL KLKVRELSEL VLSEDISNDL
160 170 180 190 200
PPVRWIRINP LKCHPNGETE PVLAELRKKF TLKVDKWSEL VPGSIYYDEF
210 220 230 240 250
IPNLFGIHPS DKITAHELYK HGKIIIQDRA SCFPAHILNP GPSDIVIDSC
260 270 280 290 300
SAPGNKTTHT ASYIYPEPPK DNNTRIYAFE KDPERAKVLQ KMIKIAGCSP
310 320 330 340 350
NISVNVGDFT KLATPEKYKD VTCFIVDPSC SGSGIFGRKF FDSFNRRKID
360 370 380 390 400
DKDDDGGIVP DEQEEFIAKE ELQTRLAKLS SFQFQMVKHA MSFPAAKKIV
410 420 430 440 450
YSTCSIHAEE NERVVIDLLL DKSVREWGWK VAPKREVIPS WPRRGKVEEF
460 470 480 490
EEVFRDGVTY DPQQLAEGCI RALPKSDGGI GFFAVCFERD
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. 44 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.
InParanoidi P53972.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 95 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