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Protein

Ribosomal lysine N-methyltransferase 1

Gene

RKM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent protein-lysine N-methyltransferase that monomethylates ribosomal protein S18 (RPS18A and RPS18B) at 'Lys-48' and dimethylates ribosomal protein L23 (RPL23A and RPL23B) at 'Lys-106' and 'Lys-110'.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei273 – 2731S-adenosyl-L-methioninePROSITE-ProRule annotation

GO - Molecular functioni

  • protein-lysine N-methyltransferase activity Source: SGD

GO - Biological processi

  • peptidyl-lysine dimethylation Source: SGD
  • peptidyl-lysine monomethylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciYEAST:G3O-34099-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal lysine N-methyltransferase 11 Publication (EC:2.1.1.-2 Publications)
Gene namesi
Name:RKM11 Publication
Ordered Locus Names:YPL208WImported
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL208W.
SGDiS000006129. RKM1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 583583Ribosomal lysine N-methyltransferase 1PRO_0000228984Add
BLAST

Proteomic databases

MaxQBiQ08961.
PeptideAtlasiQ08961.

PTM databases

iPTMnetiQ08961.

Interactioni

Protein-protein interaction databases

BioGridi35977. 19 interactions.
DIPiDIP-3971N.
IntActiQ08961. 4 interactions.
MINTiMINT-504551.

Structurei

3D structure databases

ProteinModelPortaliQ08961.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini22 – 274253SETPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili378 – 40730Sequence analysisAdd
BLAST
Coiled coili433 – 45927Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily. RKM1 family.PROSITE-ProRule annotationCurated
Contains 1 SET domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

GeneTreeiENSGT00630000090454.
HOGENOMiHOG000142041.
InParanoidiQ08961.
OMAiYLWASLI.
OrthoDBiEOG7XSTQQ.

Family and domain databases

InterProiIPR017119. Efm1/Rkm1.
IPR001214. SET_dom.
[Graphical view]
PIRSFiPIRSF037136. Ribosomal_Lys-mtfrase-1. 1 hit.
PROSITEiPS50280. SET. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08961-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSDALKALL QWGASFGVIV PEELKFLYTD LKGIICVCEK DIDNPSIKIP
60 70 80 90 100
PEIVISRNLP MKFFGLSEST KNINGWLKLF FAKIKFDRDN DTIVDNVRVN
110 120 130 140 150
DKFKPYLDAL PSRLNSPLVW NPSELKRLSS TNIGNSIHEK FEGIFKEWFE
160 170 180 190 200
LVSSSDMFDL ERVADDVQTF HNLDELTYEA LYEKILKITE LQRPTIWYSF
210 220 230 240 250
PAFLWSHLIF ISRAFPEYVL NRNCPDNSIV LLPIVDLLNH DYRSKVKWYP
260 270 280 290 300
ENGWFCYEKI GTASQSRELS NNYGGKGNEE LLSGYGFVLE DNIFDSVALK
310 320 330 340 350
VKLPLDVVST ILETEPSLKL PLLSDYTTYA FENKDCVQQE KKATRSATDY
360 370 380 390 400
INGVTYFINI QNEQCLEPLL DLFTYLSKAE EEDLHDLRAR LQGIQMLRNA
410 420 430 440 450
LQSKLNSITG PPATDDSYAI DPYRVYCADV YTKGQKQILK EALTRLKKLE
460 470 480 490 500
KTMLSENKHQ LLTMSKILKN DPAFAETELP SLFSNEDGEE VIFESTYDLL
510 520 530 540 550
ILWILLKTKK NSYPTKYEWV GQQYTNFKQT AYISDDAKAF HTAYFEKQDD
560 570 580
VDLAEVDHAI QFVVDNSFTR TSSTTEETIL VRK
Length:583
Mass (Da):67,178
Last modified:November 1, 1996 - v1
Checksum:iDB47FD895A895B31
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73564 Genomic DNA. Translation: CAA97923.1.
BK006949 Genomic DNA. Translation: DAA11228.1.
PIRiS65227.
RefSeqiNP_015116.1. NM_001184022.1.

Genome annotation databases

EnsemblFungiiYPL208W; YPL208W; YPL208W.
GeneIDi855893.
KEGGisce:YPL208W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73564 Genomic DNA. Translation: CAA97923.1.
BK006949 Genomic DNA. Translation: DAA11228.1.
PIRiS65227.
RefSeqiNP_015116.1. NM_001184022.1.

3D structure databases

ProteinModelPortaliQ08961.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35977. 19 interactions.
DIPiDIP-3971N.
IntActiQ08961. 4 interactions.
MINTiMINT-504551.

PTM databases

iPTMnetiQ08961.

Proteomic databases

MaxQBiQ08961.
PeptideAtlasiQ08961.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL208W; YPL208W; YPL208W.
GeneIDi855893.
KEGGisce:YPL208W.

Organism-specific databases

EuPathDBiFungiDB:YPL208W.
SGDiS000006129. RKM1.

Phylogenomic databases

GeneTreeiENSGT00630000090454.
HOGENOMiHOG000142041.
InParanoidiQ08961.
OMAiYLWASLI.
OrthoDBiEOG7XSTQQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-34099-MONOMER.

Miscellaneous databases

PROiQ08961.

Family and domain databases

InterProiIPR017119. Efm1/Rkm1.
IPR001214. SET_dom.
[Graphical view]
PIRSFiPIRSF037136. Ribosomal_Lys-mtfrase-1. 1 hit.
PROSITEiPS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  5. "A novel SET domain methyltransferase modifies ribosomal protein Rpl23ab in yeast."
    Porras-Yakushi T.R., Whitelegge J.P., Miranda T.B., Clarke S.
    J. Biol. Chem. 280:34590-34598(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  6. "Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily: identification of Rpl23ab methylation sites and recognition motifs."
    Porras-Yakushi T.R., Whitelegge J.P., Clarke S.
    J. Biol. Chem. 282:12368-12376(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases."
    Couttas T.A., Raftery M.J., Padula M.P., Herbert B.R., Wilkins M.R.
    Proteomics 12:960-972(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiRKM1_YEAST
AccessioniPrimary (citable) accession number: Q08961
Secondary accession number(s): D6W3G2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 106 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 4800 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 XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: 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.