RKM4_YEAST
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 03-AUG-2022, entry version 153.
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; Saccharomycetes;
OC 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., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., 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., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and 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., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT 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.13.10.6304-6313.1993;
RA Leonhardt S.A., Fearon K., Danese P.N., Mason T.L.;
RT "HSP78 encodes a yeast mitochondrial heat shock protein in the Clp family
RT 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., Dephoure N.,
RA 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 Rpl23ab in
RT 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., Wilkins M.R.;
RT "Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights
RT 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 (RPL42A
CC 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 medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. SETD6 subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00190, ECO:0000305}.
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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 AlphaFoldDB; Q12504; -.
DR SMR; Q12504; -.
DR BioGRID; 32307; 79.
DR IntAct; Q12504; 4.
DR STRING; 4932.YDR257C; -.
DR iPTMnet; Q12504; -.
DR MaxQB; Q12504; -.
DR PaxDb; Q12504; -.
DR PRIDE; Q12504; -.
DR EnsemblFungi; YDR257C_mRNA; YDR257C; YDR257C.
DR GeneID; 851844; -.
DR KEGG; sce:YDR257C; -.
DR SGD; S000002665; RKM4.
DR VEuPathDB; FungiDB:YDR257C; -.
DR eggNOG; KOG1338; Eukaryota.
DR GeneTree; ENSGT00940000153577; -.
DR HOGENOM; CLU_017135_0_0_1; -.
DR InParanoid; Q12504; -.
DR OMA; WEGLIIC; -.
DR BioCyc; YEAST:G3O-29828-MON; -.
DR Reactome; R-SCE-3214841; PKMTs methylate histone lysines.
DR ChiTaRS; RKM4; yeast.
DR PRO; PR:Q12504; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q12504; protein.
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 CDD; cd19178; SET_SETD6; 1.
DR InterPro; IPR011383; N-lys_methylase_SETD6.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR044430; SETD6_SET.
DR Pfam; PF00856; SET; 1.
DR PIRSF; PIRSF011771; RMS1_SET; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..494
FT /note="Ribosomal lysine N-methyltransferase 4"
FT /id="PRO_0000097367"
FT DOMAIN 25..265
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 264
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT CONFLICT 10..13
FT /note="NFVC -> KLCF (in Ref. 5; L16533)"
FT /evidence="ECO:0000305"
FT CONFLICT 168..174
FT /note="RVATSFE -> TCVANCPSK (in Ref. 1; CAA86307)"
FT /evidence="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
