RL12B_YEAST
ID RL12B_YEAST Reviewed; 165 AA.
AC P0CX54; D3DLJ6; P05741; P17079;
DT 28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=60S ribosomal protein L12-B {ECO:0000303|PubMed:9559554};
DE AltName: Full=L15;
DE AltName: Full=Large ribosomal subunit protein uL11-B {ECO:0000303|PubMed:24524803};
DE AltName: Full=YL23;
GN Name=RPL12B {ECO:0000303|PubMed:9559554}; Synonyms=RPL15A;
GN OrderedLocusNames=YDR418W; ORFNames=D9461.7;
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 [GENOMIC DNA].
RC STRAIN=Y166;
RX PubMed=2167467; DOI=10.1093/nar/18.15.4409;
RA Pucciarelli G., Remacha M., Ballesta J.P.G.;
RT "The 26S rRNA binding ribosomal protein equivalent to bacterial protein L11
RT is encoded by unspliced duplicated genes in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 18:4409-4416(1990).
RN [2]
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 PROTEIN SEQUENCE OF 2-16, METHYLATION AT LYS-4, METHYLATION AT LYS-11 BY
RP RKM2, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17005568; DOI=10.1074/jbc.m606578200;
RA Porras-Yakushi T.R., Whitelegge J.P., Clarke S.;
RT "A novel SET domain methyltransferase in yeast: Rkm2-dependent
RT trimethylation of ribosomal protein L12ab at lysine 10.";
RL J. Biol. Chem. 281:35835-35845(2006).
RN [5]
RP PARTIAL PROTEIN SEQUENCE OF 17-36.
RX PubMed=18782943; DOI=10.1007/bf00341461;
RA Otaka E., Higo K., Itoh T.;
RT "Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence
RT characterization of twenty-four proteins from cytoplasmic ribosomes.";
RL Mol. Gen. Genet. 195:544-546(1984).
RN [6]
RP NOMENCLATURE, AND SUBUNIT.
RX PubMed=9559554;
RX DOI=10.1002/(sici)1097-0061(19980330)14:5<471::aid-yea241>3.0.co;2-u;
RA Planta R.J., Mager W.H.;
RT "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae.";
RL Yeast 14:471-477(1998).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, METHYLATION AT ARG-67, AND MUTAGENESIS
RP OF ARG-67.
RX PubMed=11856739; DOI=10.1074/jbc.m111379200;
RA Chern M.-K., Chang K.-N., Liu L.-F., Tam T.-C.S., Liu Y.-C., Liang Y.-L.,
RA Tam M.F.;
RT "Yeast ribosomal protein L12 is a substrate of protein-arginine
RT methyltransferase 2.";
RL J. Biol. Chem. 277:15345-15353(2002).
RN [8]
RP MASS SPECTROMETRY.
RX PubMed=11983894; DOI=10.1073/pnas.082119899;
RA Lee S.-W., Berger S.J., Martinovic S., Pasa-Tolic L., Anderson G.A.,
RA Shen Y., Zhao R., Smith R.D.;
RT "Direct mass spectrometric analysis of intact proteins of the yeast large
RT ribosomal subunit using capillary LC/FTICR.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:5942-5947(2002).
RN [9]
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 [10]
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 [11]
RP METHYLATION AT PRO-2 AND ARG-67, AND METHYLATION AT LYS-4 BY RKM2.
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 [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, AND IDENTIFICATION BY
RP 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 [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-25 AND SER-38, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [14]
RP METHYLATION AT PRO-2 BY NTM1/TAE1.
RX PubMed=20481588; DOI=10.1021/bi100428x;
RA Webb K.J., Lipson R.S., Al-Hadid Q., Whitelegge J.P., Clarke S.G.;
RT "Identification of protein N-terminal methyltransferases in yeast and
RT humans.";
RL Biochemistry 49:5225-5235(2010).
RN [15]
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=22096102; DOI=10.1126/science.1212642;
RA Ben-Shem A., Garreau de Loubresse N., Melnikov S., Jenner L., Yusupova G.,
RA Yusupov M.;
RT "The structure of the eukaryotic ribosome at 3.0 A resolution.";
RL Science 334:1524-1529(2011).
RN [16]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-130 AND LYS-146, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
RN [17]
RP NOMENCLATURE.
RX PubMed=24524803; DOI=10.1016/j.sbi.2014.01.002;
RA Ban N., Beckmann R., Cate J.H.D., Dinman J.D., Dragon F., Ellis S.R.,
RA Lafontaine D.L.J., Lindahl L., Liljas A., Lipton J.M., McAlear M.A.,
RA Moore P.B., Noller H.F., Ortega J., Panse V.G., Ramakrishnan V.,
RA Spahn C.M.T., Steitz T.A., Tchorzewski M., Tollervey D., Warren A.J.,
RA Williamson J.R., Wilson D., Yonath A., Yusupov M.;
RT "A new system for naming ribosomal proteins.";
RL Curr. Opin. Struct. Biol. 24:165-169(2014).
CC -!- FUNCTION: Component of the ribosome, a large ribonucleoprotein complex
CC responsible for the synthesis of proteins in the cell. The small
CC ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the
CC encoded message by selecting cognate aminoacyl-transfer RNA (tRNA)
CC molecules. The large subunit (LSU) contains the ribosomal catalytic
CC site termed the peptidyl transferase center (PTC), which catalyzes the
CC formation of peptide bonds, thereby polymerizing the amino acids
CC delivered by tRNAs into a polypeptide chain. The nascent polypeptides
CC leave the ribosome through a tunnel in the LSU and interact with
CC protein factors that function in enzymatic processing, targeting, and
CC the membrane insertion of nascent chains at the exit of the ribosomal
CC tunnel. {ECO:0000305|PubMed:22096102}.
CC -!- SUBUNIT: Component of the large ribosomal subunit (LSU). Mature yeast
CC ribosomes consist of a small (40S) and a large (60S) subunit. The 40S
CC small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33
CC different proteins (encoded by 57 genes). The large 60S subunit
CC contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different
CC proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102).
CC {ECO:0000269|PubMed:22096102, ECO:0000305|PubMed:9559554}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:22096102}.
CC -!- PTM: It appears that the main modified species for L12 contains 6
CC methyl groups, 2 on Pro-2, 3 on Lys-4 and 1 on Arg-67. Although not
CC reproduced with a second method, methylation at Lys-11 cannot be ruled
CC out. {ECO:0000269|PubMed:11856739, ECO:0000269|PubMed:17005568,
CC ECO:0000269|PubMed:18957409, ECO:0000269|PubMed:20481588}.
CC -!- MASS SPECTROMETRY: Mass=17764.712; Method=Electrospray;
CC Note=Monoisotopic mass with either 6 methylation modifications or 1
CC acetylation and 3 methylation modifications.;
CC Evidence={ECO:0000269|PubMed:11983894};
CC -!- MISCELLANEOUS: Present with 50300 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- MISCELLANEOUS: There are 2 genes for uL11 in yeast. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL11 family.
CC {ECO:0000305}.
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DR EMBL; X51520; CAA35892.1; -; Genomic_DNA.
DR EMBL; U33007; AAB64852.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12258.1; -; Genomic_DNA.
DR PIR; S13665; S13665.
DR RefSeq; NP_010706.3; NM_001180726.3.
DR RefSeq; NP_010860.1; NM_001178869.1.
DR AlphaFoldDB; P0CX54; -.
DR SMR; P0CX54; -.
DR BioGRID; 32476; 121.
DR BioGRID; 36675; 181.
DR IntAct; P0CX54; 2.
DR MINT; P0CX54; -.
DR iPTMnet; P0CX54; -.
DR PRIDE; P0CX54; -.
DR EnsemblFungi; YDR418W_mRNA; YDR418W; YDR418W.
DR EnsemblFungi; YEL054C_mRNA; YEL054C; YEL054C.
DR GeneID; 852026; -.
DR GeneID; 856656; -.
DR KEGG; sce:YDR418W; -.
DR KEGG; sce:YEL054C; -.
DR SGD; S000002826; RPL12B.
DR VEuPathDB; FungiDB:YDR418W; -.
DR VEuPathDB; FungiDB:YEL054C; -.
DR GeneTree; ENSGT00390000006922; -.
DR HOGENOM; CLU_074237_5_0_1; -.
DR InParanoid; P0CX54; -.
DR BioCyc; YEAST:G3O-29959-MON; -.
DR Reactome; R-SCE-156827; L13a-mediated translational silencing of Ceruloplasmin expression.
DR Reactome; R-SCE-1799339; SRP-dependent cotranslational protein targeting to membrane.
DR Reactome; R-SCE-72689; Formation of a pool of free 40S subunits.
DR Reactome; R-SCE-72706; GTP hydrolysis and joining of the 60S ribosomal subunit.
DR Reactome; R-SCE-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-SCE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR PRO; PR:P0CX54; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P0CX54; protein.
DR ExpressionAtlas; P0CX54; baseline and differential.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IDA:SGD.
DR GO; GO:0015934; C:large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0070180; F:large ribosomal subunit rRNA binding; IBA:GO_Central.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0002181; P:cytoplasmic translation; IC:SGD.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD.
DR GO; GO:0006412; P:translation; IBA:GO_Central.
DR CDD; cd00349; Ribosomal_L11; 1.
DR Gene3D; 1.10.10.250; -; 1.
DR Gene3D; 3.30.1550.10; -; 1.
DR HAMAP; MF_00736; Ribosomal_L11; 1.
DR InterPro; IPR000911; Ribosomal_L11/L12.
DR InterPro; IPR036796; Ribosomal_L11/L12_N_sf.
DR InterPro; IPR020783; Ribosomal_L11_C.
DR InterPro; IPR036769; Ribosomal_L11_C_sf.
DR InterPro; IPR020785; Ribosomal_L11_CS.
DR InterPro; IPR020784; Ribosomal_L11_N.
DR PANTHER; PTHR11661; PTHR11661; 1.
DR Pfam; PF00298; Ribosomal_L11; 1.
DR Pfam; PF03946; Ribosomal_L11_N; 1.
DR SMART; SM00649; RL11; 1.
DR SUPFAM; SSF46906; SSF46906; 1.
DR SUPFAM; SSF54747; SSF54747; 1.
DR PROSITE; PS00359; RIBOSOMAL_L11; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Direct protein sequencing; Isopeptide bond; Methylation;
KW Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosomal protein;
KW RNA-binding; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:17005568"
FT CHAIN 2..165
FT /note="60S ribosomal protein L12-B"
FT /id="PRO_0000409773"
FT MOD_RES 2
FT /note="N,N-dimethylproline; by NTM1"
FT /evidence="ECO:0000269|PubMed:18957409,
FT ECO:0000269|PubMed:20481588"
FT MOD_RES 4
FT /note="N6,N6,N6-trimethyllysine; by RKM2"
FT /evidence="ECO:0000269|PubMed:17005568,
FT ECO:0000269|PubMed:18957409"
FT MOD_RES 11
FT /note="N6,N6,N6-trimethyllysine; by RKM2"
FT /evidence="ECO:0000269|PubMed:17005568"
FT MOD_RES 25
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 38
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 67
FT /note="N5-methylarginine; by RMT2"
FT /evidence="ECO:0000269|PubMed:11856739,
FT ECO:0000269|PubMed:18957409"
FT CROSSLNK 130
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT CROSSLNK 146
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT MUTAGEN 67
FT /note="R->K: Abolishes monomethylation by RMT2."
FT /evidence="ECO:0000269|PubMed:11856739"
SQ SEQUENCE 165 AA; 17823 MW; 0B23A483781DFBE5 CRC64;
MPPKFDPNEV KYLYLRAVGG EVGASAALAP KIGPLGLSPK KVGEDIAKAT KEFKGIKVTV
QLKIQNRQAA ASVVPSASSL VITALKEPPR DRKKDKNVKH SGNIQLDEII EIARQMRDKS
FGRTLASVTK EILGTAQSVG CRVDFKNPHD IIEGINAGEI EIPEN
