RKM1_YEAST
ID RKM1_YEAST Reviewed; 583 AA.
AC Q08961; D6W3G2;
DT 21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Ribosomal lysine N-methyltransferase 1 {ECO:0000303|PubMed:16096273};
DE EC=2.1.1.- {ECO:0000269|PubMed:16096273, ECO:0000269|PubMed:22522802};
GN Name=RKM1 {ECO:0000303|PubMed:16096273};
GN OrderedLocusNames=YPL208W {ECO:0000312|SGD:S000006129};
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]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
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 [3]
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 [4]
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 [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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 [6]
RP FUNCTION.
RX PubMed=17327221; DOI=10.1074/jbc.m611896200;
RA Porras-Yakushi T.R., Whitelegge J.P., Clarke S.;
RT "Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily:
RT identification of Rpl23ab methylation sites and recognition motifs.";
RL J. Biol. Chem. 282:12368-12376(2007).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [8]
RP FUNCTION.
RX PubMed=22522802; DOI=10.1002/pmic.201100570;
RA Couttas T.A., Raftery M.J., Padula M.P., Herbert B.R., Wilkins M.R.;
RT "Methylation of translation-associated proteins in Saccharomyces
RT cerevisiae: Identification of methylated lysines and their
RT methyltransferases.";
RL Proteomics 12:960-972(2012).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent protein-lysine N-
CC methyltransferase that monomethylates ribosomal protein S18 (RPS18A and
CC RPS18B) at 'Lys-48' and dimethylates ribosomal protein L23 (RPL23A and
CC RPL23B) at 'Lys-106' and 'Lys-110'. {ECO:0000269|PubMed:16096273,
CC ECO:0000269|PubMed:22522802}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 4800 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. RKM1 family. {ECO:0000255|PROSITE-ProRule:PRU00190,
CC ECO:0000305}.
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DR EMBL; Z73564; CAA97923.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11228.1; -; Genomic_DNA.
DR PIR; S65227; S65227.
DR RefSeq; NP_015116.1; NM_001184022.1.
DR AlphaFoldDB; Q08961; -.
DR BioGRID; 35977; 40.
DR DIP; DIP-3971N; -.
DR IntAct; Q08961; 4.
DR MINT; Q08961; -.
DR STRING; 4932.YPL208W; -.
DR iPTMnet; Q08961; -.
DR MaxQB; Q08961; -.
DR PaxDb; Q08961; -.
DR PRIDE; Q08961; -.
DR EnsemblFungi; YPL208W_mRNA; YPL208W; YPL208W.
DR GeneID; 855893; -.
DR KEGG; sce:YPL208W; -.
DR SGD; S000006129; RKM1.
DR VEuPathDB; FungiDB:YPL208W; -.
DR eggNOG; KOG1337; Eukaryota.
DR GeneTree; ENSGT00940000153577; -.
DR HOGENOM; CLU_030667_2_0_1; -.
DR InParanoid; Q08961; -.
DR OMA; FLWSHLI; -.
DR BioCyc; YEAST:G3O-34099-MON; -.
DR PRO; PR:Q08961; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q08961; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0016279; F:protein-lysine N-methyltransferase activity; IDA:SGD.
DR GO; GO:0018027; P:peptidyl-lysine dimethylation; IDA:SGD.
DR GO; GO:0018026; P:peptidyl-lysine monomethylation; IMP:SGD.
DR InterPro; IPR017119; Efm1/Rkm1.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR PIRSF; PIRSF037136; Ribosomal_Lys-mtfrase-1; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Cytoplasm; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..583
FT /note="Ribosomal lysine N-methyltransferase 1"
FT /id="PRO_0000228984"
FT DOMAIN 22..274
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT COILED 378..407
FT /evidence="ECO:0000255"
FT COILED 433..459
FT /evidence="ECO:0000255"
FT BINDING 273
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
SQ SEQUENCE 583 AA; 67178 MW; DB47FD895A895B31 CRC64;
MSSDALKALL QWGASFGVIV PEELKFLYTD LKGIICVCEK DIDNPSIKIP PEIVISRNLP
MKFFGLSEST KNINGWLKLF FAKIKFDRDN DTIVDNVRVN DKFKPYLDAL PSRLNSPLVW
NPSELKRLSS TNIGNSIHEK FEGIFKEWFE LVSSSDMFDL ERVADDVQTF HNLDELTYEA
LYEKILKITE LQRPTIWYSF PAFLWSHLIF ISRAFPEYVL NRNCPDNSIV LLPIVDLLNH
DYRSKVKWYP ENGWFCYEKI GTASQSRELS NNYGGKGNEE LLSGYGFVLE DNIFDSVALK
VKLPLDVVST ILETEPSLKL PLLSDYTTYA FENKDCVQQE KKATRSATDY INGVTYFINI
QNEQCLEPLL DLFTYLSKAE EEDLHDLRAR LQGIQMLRNA LQSKLNSITG PPATDDSYAI
DPYRVYCADV YTKGQKQILK EALTRLKKLE KTMLSENKHQ LLTMSKILKN DPAFAETELP
SLFSNEDGEE VIFESTYDLL ILWILLKTKK NSYPTKYEWV GQQYTNFKQT AYISDDAKAF
HTAYFEKQDD VDLAEVDHAI QFVVDNSFTR TSSTTEETIL VRK
