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Protein

25S rRNA (cytosine(2870)-C(5))-methyltransferase

Gene

NOP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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 2870 (m5C2870) in 25S rRNA. Required for 60S ribosomal subunit synthesis and processing.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + cytosine(2870) in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(2870) in 25S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei377 – 3771S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei404 – 4041S-adenosyl-L-methioninePROSITE-ProRule annotation
Binding sitei421 – 4211S-adenosyl-L-methioninePROSITE-ProRule annotation
Active sitei478 – 4781NucleophilePROSITE-ProRule annotation

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • rRNA (cytosine-C5-)-methyltransferase activity Source: SGD

GO - Biological processi

  • assembly of large subunit precursor of preribosome Source: SGD
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • ribosomal large subunit biogenesis Source: SGD
  • rRNA base methylation Source: SGD
  • rRNA methylation Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciYEAST:G3O-33091-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.

Names & Taxonomyi

Protein namesi
Recommended name:
25S rRNA (cytosine(2870)-C(5))-methyltransferase (EC:2.1.1.3101 Publication)
Alternative name(s):
Nucleolar protein 2
Gene namesi
Name:NOP2
Synonyms:YNA1
Ordered Locus Names:YNL061W
ORF Names:N2428, YNL2428W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL061W.
SGDiS000005005. NOP2.

Subcellular locationi

GO - Cellular componenti

  • nucleolus Source: SGD
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi424 – 4241C → A or S: Cannot complement loss of wild type NOP2. 2 Publications
Mutagenesisi478 – 4781C → A: Fails to ctalyze the C-5 methylation of the C2870 residue and strongly affects 60S biogenesis. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 61861825S rRNA (cytosine(2870)-C(5))-methyltransferasePRO_0000211819Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei580 – 5801PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP40991.

PTM databases

iPTMnetiP40991.

Interactioni

Subunit structurei

Interacts with NOP53. Interacts with TRM112.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NOG1Q028923EBI-12110,EBI-12105

Protein-protein interaction databases

BioGridi35762. 130 interactions.
DIPiDIP-6488N.
IntActiP40991. 55 interactions.
MINTiMINT-612803.

Structurei

3D structure databases

ProteinModelPortaliP40991.
SMRiP40991. Positions 228-549.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni353 – 3597S-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

GeneTreeiENSGT00660000095341.
HOGENOMiHOG000224258.
InParanoidiP40991.
KOiK14835.
OMAiIIYANEI.
OrthoDBiEOG74FF8R.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR023273. RCMT_NOP2.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
PR02012. RCMTNOP2.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40991-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSRRHKNKQ AAPPTLEEFQ ARKEKKANRK LEKGKRPSTT QGDEVSDRKK
60 70 80 90 100
KKSKPFKKSR KEEEEVVEED KDLPEVDLEE LSKARKSLFD DEEDDDEAGL
110 120 130 140 150
VDEELKDEFD LEQEYDYDED EDNDAHPIFS DDDDEADLEE LNAQNMEALS
160 170 180 190 200
KKLDEEEAEE AEEAEMELVE AENMQPRADI LPTEEQEEMM AQETPNLTST
210 220 230 240 250
RTRMIEIVKV LENFKTLGAE GRSRGEYVDR LLKDICEYFG YTPFLAEKLF
260 270 280 290 300
NLFSPAEAME FFEANEIARP ITIRTNTLKT RRRDLAQTLV NRGVNLQPIG
310 320 330 340 350
SWTKVGLQIF DSQVPIGATP EYLAGHYILQ AASSFLPVIA LDPHENERIL
360 370 380 390 400
DMAAAPGGKT TYISAMMKNT GCVFANDANK SRTKSLIANI HRLGCTNTIV
410 420 430 440 450
CNYDAREFPK VIGGFDRILL DAPCSGTGVI GKDQSVKVSR TEKDFIQIPH
460 470 480 490 500
LQKQLLLSAI DSVDCNSKHG GVIVYSTCSV AVEEDEAVID YALRKRPNVK
510 520 530 540 550
LVDTGLAIGK EAFTSYRGKK FHPSVKLARR YYPHTYNVDG FFVAKFQKIG
560 570 580 590 600
PSSFDDNQAS AKEKETAARK EALEEGIIHS DFATFEDEED DKYIEKSVKN
610
NLLKKGVNPK AKRPSNEK
Length:618
Mass (Da):69,812
Last modified:February 1, 1995 - v1
Checksum:i6D11575703C6BB8B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti216 – 2161T → A in AAT93079 (PubMed:17322287).Curated
Sequence conflicti577 – 5771I → M in CAA58502 (Ref. 6) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82656 Genomic DNA. Translation: CAA57979.1.
U12141 Genomic DNA. Translation: AAA99650.1.
Z71337 Genomic DNA. Translation: CAA95934.1.
AY693060 Genomic DNA. Translation: AAT93079.1.
X83512 Genomic DNA. Translation: CAA58502.1.
BK006947 Genomic DNA. Translation: DAA10485.1.
PIRiA55188.
RefSeqiNP_014338.3. NM_001182899.3.

Genome annotation databases

EnsemblFungiiYNL061W; YNL061W; YNL061W.
GeneIDi855664.
KEGGisce:YNL061W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82656 Genomic DNA. Translation: CAA57979.1.
U12141 Genomic DNA. Translation: AAA99650.1.
Z71337 Genomic DNA. Translation: CAA95934.1.
AY693060 Genomic DNA. Translation: AAT93079.1.
X83512 Genomic DNA. Translation: CAA58502.1.
BK006947 Genomic DNA. Translation: DAA10485.1.
PIRiA55188.
RefSeqiNP_014338.3. NM_001182899.3.

3D structure databases

ProteinModelPortaliP40991.
SMRiP40991. Positions 228-549.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35762. 130 interactions.
DIPiDIP-6488N.
IntActiP40991. 55 interactions.
MINTiMINT-612803.

PTM databases

iPTMnetiP40991.

Proteomic databases

MaxQBiP40991.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL061W; YNL061W; YNL061W.
GeneIDi855664.
KEGGisce:YNL061W.

Organism-specific databases

EuPathDBiFungiDB:YNL061W.
SGDiS000005005. NOP2.

Phylogenomic databases

GeneTreeiENSGT00660000095341.
HOGENOMiHOG000224258.
InParanoidiP40991.
KOiK14835.
OMAiIIYANEI.
OrthoDBiEOG74FF8R.

Enzyme and pathway databases

BioCyciYEAST:G3O-33091-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus.

Miscellaneous databases

PROiP40991.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR023273. RCMT_NOP2.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
PR02012. RCMTNOP2.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Yeast NOP2 encodes an essential nucleolar protein with homology to a human proliferation marker."
    de Beus E., Brockenbrough J.S., Hong B., Aris J.P.
    J. Cell Biol. 127:1799-1813(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: BJ2168.
  2. "The sequence of a 44 420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae."
    Bergez P., Doignon F., Crouzet M.
    Yeast 11:967-974(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: S288c / FY1676.
  3. "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.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. Garcia-Barrio M.T., Cuesta R., Hinnebusch A.G., Tamame Gonzalez M.
    Submitted (DEC-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 146-618.
    Strain: ATCC 204508 / S288c.
  7. "A conserved motif in the yeast nucleolar protein Nop2p contains an essential cysteine residue."
    King M., Ton D., Redman K.L.
    Biochem. J. 337:29-35(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-424 AND CYS-478, FUNCTION.
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein."
    Sydorskyy Y., Dilworth D.J., Halloran B., Yi E.C., Makhnevych T., Wozniak R.W., Aitchison J.D.
    Biochem. J. 388:819-826(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NOP53, IDENTIFICATION BY MASS SPECTROMETRY.
  10. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-580, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "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.
  13. "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, MUTAGENESIS OF CYS-424 AND CYS-478.

Entry informationi

Entry nameiNOP2_YEAST
AccessioniPrimary (citable) accession number: P40991
Secondary accession number(s): D6W1B9, E9P914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 6, 2016
This is version 142 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 18700 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.