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Database: UniProt
Entry: Q12504
LinkDB: Q12504
Original site: Q12504 
ID   RKM4_YEAST              Reviewed;         494 AA.
AC   Q12504; D6VSN7; Q07015;
DT   26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   13-FEB-2019, entry version 137.
DE   RecName: Full=Ribosomal lysine N-methyltransferase 4 {ECO:0000303|PubMed:18957409};
DE            EC=2.1.1.- {ECO:0000269|PubMed:18957409, ECO:0000269|PubMed:24517342};
DE   AltName: Full=SET domain-containing protein 7 {ECO:0000303|PubMed:16096273};
GN   Name=RKM4 {ECO:0000303|PubMed:18957409};
GN   Synonyms=RMS1 {ECO:0000312|EMBL:CAA86307.1},
GN   SET7 {ECO:0000303|PubMed:16096273};
GN   OrderedLocusNames=YDR257C {ECO:0000312|SGD:S000002665};
GN   ORFNames=YD9320A.07C;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1] {ECO:0000305}
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Pavlik P.;
RT   "Characterization of RMS1 gene.";
RL   Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000305}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169867;
RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N.,
RA   Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M.,
RA   Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L.,
RA   Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M.,
RA   Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S.,
RA   Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M.,
RA   Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S.,
RA   Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K.,
RA   Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D.,
RA   Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C.,
RA   Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T.,
RA   Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E.,
RA   Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W.,
RA   Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K.,
RA   Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S.,
RA   Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A.,
RA   Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S.,
RA   Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M.,
RA   Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y.,
RA   Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M.,
RA   Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E.,
RA   Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R.,
RA   Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA   Mewes H.-W., Zollner A., Zaccaria P.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL   Nature 387:75-78(1997).
RN   [3]
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.,
RA   Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and
RT   now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=17322287; DOI=10.1101/gr.6037607;
RA   Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA   Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
RA   Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
RA   Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
RA   Kolodner R.D., LaBaer J.;
RT   "Approaching a complete repository of sequence-verified protein-
RT   encoding clones for Saccharomyces cerevisiae.";
RL   Genome Res. 17:536-543(2007).
RN   [5] {ECO:0000305}
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-32.
RX   PubMed=8413229; DOI=10.1128/MCB.13.10.6304;
RA   Leonhardt S.A., Fearon K., Danese P.N., Mason T.L.;
RT   "HSP78 encodes a yeast mitochondrial heat shock protein in the Clp
RT   family of ATP-dependent proteases.";
RL   Mol. Cell. Biol. 13:6304-6313(1993).
RN   [6] {ECO:0000305}
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [7]
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.,
RA   Dephoure N., O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [8]
RP   GENE NAME.
RX   PubMed=16096273; DOI=10.1074/jbc.M507672200;
RA   Porras-Yakushi T.R., Whitelegge J.P., Miranda T.B., Clarke S.;
RT   "A novel SET domain methyltransferase modifies ribosomal protein
RT   Rpl23ab in yeast.";
RL   J. Biol. Chem. 280:34590-34598(2005).
RN   [9]
RP   FUNCTION.
RX   PubMed=18957409; DOI=10.1074/jbc.M806006200;
RA   Webb K.J., Laganowsky A., Whitelegge J.P., Clarke S.G.;
RT   "Identification of two SET domain proteins required for methylation of
RT   lysine residues in yeast ribosomal protein Rpl42ab.";
RL   J. Biol. Chem. 283:35561-35568(2008).
RN   [10]
RP   FUNCTION.
RX   PubMed=24517342; DOI=10.1021/pr401251k;
RA   Hart-Smith G., Chia S.Z., Low J.K., McKay M.J., Molloy M.P.,
RA   Wilkins M.R.;
RT   "Stoichiometry of Saccharomyces cerevisiae lysine methylation:
RT   insights into non-histone protein lysine methyltransferase activity.";
RL   J. Proteome Res. 13:1744-1756(2014).
CC   -!- FUNCTION: S-adenosyl-L-methionine-dependent protein-lysine N-
CC       methyltransferase that monomethylates 60S ribosomal protein L42
CC       (RPL42A and RPL42B) at 'Lys-55'. {ECO:0000269|PubMed:18957409,
CC       ECO:0000269|PubMed:24517342}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC   -!- MISCELLANEOUS: Present with 4010 molecules/cell in log phase SD
CC       medium. {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. Histone-lysine methyltransferase
CC       family. SETD6 subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190,
CC       ECO:0000305}.
DR   EMBL; Z46237; CAA86307.1; -; Genomic_DNA.
DR   EMBL; Z70202; CAA94096.1; -; Genomic_DNA.
DR   EMBL; Z68329; CAA92714.1; -; Genomic_DNA.
DR   EMBL; AY723787; AAU09704.1; -; Genomic_DNA.
DR   EMBL; L16533; -; NOT_ANNOTATED_CDS; Unassigned_DNA.
DR   EMBL; BK006938; DAA12097.1; -; Genomic_DNA.
DR   PIR; S67314; S67314.
DR   RefSeq; NP_010543.1; NM_001180565.1.
DR   ProteinModelPortal; Q12504; -.
DR   BioGrid; 32307; 77.
DR   IntAct; Q12504; 4.
DR   STRING; 4932.YDR257C; -.
DR   MaxQB; Q12504; -.
DR   PaxDb; Q12504; -.
DR   PRIDE; Q12504; -.
DR   EnsemblFungi; YDR257C_mRNA; YDR257C_mRNA; YDR257C.
DR   GeneID; 851844; -.
DR   KEGG; sce:YDR257C; -.
DR   EuPathDB; FungiDB:YDR257C; -.
DR   SGD; S000002665; RKM4.
DR   GeneTree; ENSGT00940000153577; -.
DR   HOGENOM; HOG000247886; -.
DR   InParanoid; Q12504; -.
DR   KO; K05302; -.
DR   OMA; MSYSFDV; -.
DR   BioCyc; YEAST:G3O-29828-MONOMER; -.
DR   ChiTaRS; RKM4; yeast.
DR   PRO; PR:Q12504; -.
DR   Proteomes; UP000002311; Chromosome IV.
DR   GO; GO:0005634; C:nucleus; HDA:SGD.
DR   GO; GO:0016279; F:protein-lysine N-methyltransferase activity; IMP:SGD.
DR   GO; GO:0018026; P:peptidyl-lysine monomethylation; IMP:SGD.
DR   InterPro; IPR011383; N-lys_methylase_SETD6.
DR   InterPro; IPR001214; SET_dom.
DR   Pfam; PF00856; SET; 1.
DR   PIRSF; PIRSF011771; RMS1_SET; 1.
DR   PROSITE; PS50280; SET; 1.
PE   1: Evidence at protein level;
KW   Complete proteome; Methyltransferase; Nucleus; Reference proteome;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN         1    494       Ribosomal lysine N-methyltransferase 4.
FT                                /FTId=PRO_0000097367.
FT   DOMAIN       25    265       SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00190}.
FT   COMPBIAS    201    206       Poly-Glu.
FT   BINDING     264    264       S-adenosyl-L-methionine.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00190}.
FT   CONFLICT     10     13       NFVC -> KLCF (in Ref. 5; L16533).
FT                                {ECO:0000305}.
FT   CONFLICT    168    174       RVATSFE -> TCVANCPSK (in Ref. 1;
FT                                CAA86307). {ECO:0000305}.
SQ   SEQUENCE   494 AA;  57289 MW;  22034EB9DFB2440D CRC64;
     MDDFSRDTEN FVCWLKTTAE IEVSPKIEIK DLCCDNQGRA VVATQKIKKD ETLFKIPRSS
     VLSVTTSQLI KDYPSLKDKF LNETGSWEGL IICILYEMEV LQERSRWAPY FKVWNKPSDM
     NALIFWDDNE LQLLKPSLVL ERIGKKEAKE MHERIIKSIK QIGGEFSRVA TSFEFDNFAY
     IASIILSYSF DLEMQDSSVN ENEEEETSEE ELENERYLKS MIPLADMLNA DTSKCNANLT
     YDSNCLKMVA LRDIEKNEQV YNIYGEHPNS ELLRRYGYVE WDGSKYDFGE VLLENIVEAL
     KETFETNTEF LDRCIDILRN NANIQEFLEG EEIVLDSYDC YNNGELLPQL ILLVQILTIL
     CQIPGLCKLD IKAMERQVER IVKKCLQLIE GARATTNCSA TWKRCIMKRL ADYPIKKCVS
     IEKPSKGNSL TREELRDVMA RRVLKSEIDS LQVCEETIDK NYKVIPDEKL LTNILKRKLT
     EEEKSSVKRP CVKK
//
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