RL16B_YEAST
ID RL16B_YEAST Reviewed; 198 AA.
AC P26785; D6W1B0;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 190.
DE RecName: Full=60S ribosomal protein L16-B {ECO:0000303|PubMed:9559554};
DE AltName: Full=L21;
DE AltName: Full=Large ribosomal subunit protein uL13-B {ECO:0000303|PubMed:24524803};
DE AltName: Full=RP23;
DE AltName: Full=YL15;
GN Name=RPL16B {ECO:0000303|PubMed:9559554}; Synonyms=RP23, RPL21B;
GN OrderedLocusNames=YNL069C; ORFNames=N2377;
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=ATCC 96604 / S288c / FY1679;
RX PubMed=8701611;
RX DOI=10.1002/(sici)1097-0061(19960330)12:4<391::aid-yea921>3.0.co;2-n;
RA Poehlmann R., Philippsen P.;
RT "Sequencing a cosmid clone of Saccharomyces cerevisiae chromosome XIV
RT reveals 12 new open reading frames (ORFs) and an ancient duplication of six
RT ORFs.";
RL Yeast 12:391-402(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(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 2-26, AND ACETYLATION AT SER-2 BY NATA.
RX PubMed=1544921; DOI=10.1016/s0021-9258(18)42785-8;
RA Takakura H., Tsunasawa S., Miyagi M., Warner J.R.;
RT "NH2-terminal acetylation of ribosomal proteins of Saccharomyces
RT cerevisiae.";
RL J. Biol. Chem. 267:5442-5445(1992).
RN [5]
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 [6]
RP CLEAVAGE OF INITIATOR METHIONINE, AND ACETYLATION AT SER-2 BY NATA.
RX PubMed=10601260; DOI=10.1074/jbc.274.52.37035;
RA Arnold R.J., Polevoda B., Reilly J.P., Sherman F.;
RT "The action of N-terminal acetyltransferases on yeast ribosomal proteins.";
RL J. Biol. Chem. 274:37035-37040(1999).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-185 AND SER-187, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-43, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-181 AND SER-187, AND
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-185 AND SER-187, 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 [11]
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 [12]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [13]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-176, AND IDENTIFICATION BY
RP 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 [14]
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:22096102}.
CC -!- PTM: N-terminally acetylated by acetyltransferase NatA.
CC {ECO:0000269|PubMed:10601260, ECO:0000269|PubMed:1544921}.
CC -!- MISCELLANEOUS: There are 2 genes for uL13 in yeast. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL13 family.
CC {ECO:0000305}.
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DR EMBL; X86470; CAA60191.1; -; Genomic_DNA.
DR EMBL; X86470; CAA60192.1; -; Genomic_DNA.
DR EMBL; Z71345; CAA95943.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10476.1; -; Genomic_DNA.
DR PIR; S53911; S53911.
DR RefSeq; NP_014330.1; NM_001182907.1.
DR PDB; 4V88; X-ray; 3.00 A; BO/DO=4-162, BO/DO=144-182.
DR PDB; 6QIK; EM; 3.10 A; J=1-198.
DR PDB; 6QT0; EM; 3.40 A; J=1-198.
DR PDB; 6QTZ; EM; 3.50 A; J=1-198.
DR PDB; 6RI5; EM; 3.30 A; J=1-198.
DR PDB; 6RZZ; EM; 3.20 A; J=1-198.
DR PDB; 6S05; EM; 3.90 A; J=1-198.
DR PDBsum; 4V88; -.
DR PDBsum; 6QIK; -.
DR PDBsum; 6QT0; -.
DR PDBsum; 6QTZ; -.
DR PDBsum; 6RI5; -.
DR PDBsum; 6RZZ; -.
DR PDBsum; 6S05; -.
DR AlphaFoldDB; P26785; -.
DR SMR; P26785; -.
DR BioGRID; 35754; 152.
DR IntAct; P26785; 26.
DR MINT; P26785; -.
DR STRING; 4932.YNL069C; -.
DR iPTMnet; P26785; -.
DR MaxQB; P26785; -.
DR PaxDb; P26785; -.
DR PRIDE; P26785; -.
DR EnsemblFungi; YNL069C_mRNA; YNL069C; YNL069C.
DR GeneID; 855655; -.
DR KEGG; sce:YNL069C; -.
DR SGD; S000005013; RPL16B.
DR VEuPathDB; FungiDB:YNL069C; -.
DR eggNOG; KOG3204; Eukaryota.
DR GeneTree; ENSGT00390000010799; -.
DR HOGENOM; CLU_076922_0_0_1; -.
DR InParanoid; P26785; -.
DR OMA; WRTMRGM; -.
DR BioCyc; YEAST:G3O-33099-MON; -.
DR PRO; PR:P26785; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P26785; protein.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IDA:SGD.
DR GO; GO:0005840; C:ribosome; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IDA:SGD.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0002181; P:cytoplasmic translation; IC:SGD.
DR GO; GO:0017148; P:negative regulation of translation; IBA:GO_Central.
DR CDD; cd00392; Ribosomal_L13; 1.
DR Gene3D; 3.90.1180.10; -; 1.
DR HAMAP; MF_01366; Ribosomal_L13; 1.
DR InterPro; IPR005822; Ribosomal_L13.
DR InterPro; IPR023563; Ribosomal_L13_CS.
DR InterPro; IPR005755; Ribosomal_L13_euk/arc.
DR InterPro; IPR036899; Ribosomal_L13_sf.
DR PANTHER; PTHR11545; PTHR11545; 1.
DR PANTHER; PTHR11545:SF3; PTHR11545:SF3; 1.
DR Pfam; PF00572; Ribosomal_L13; 1.
DR SUPFAM; SSF52161; SSF52161; 1.
DR TIGRFAMs; TIGR01077; L13_A_E; 1.
DR PROSITE; PS00783; RIBOSOMAL_L13; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing;
KW Isopeptide bond; Phosphoprotein; Reference proteome; Ribonucleoprotein;
KW Ribosomal protein; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10601260,
FT ECO:0000269|PubMed:1544921"
FT CHAIN 2..198
FT /note="60S ribosomal protein L16-B"
FT /id="PRO_0000133792"
FT MOD_RES 2
FT /note="N-acetylserine; partial"
FT /evidence="ECO:0000269|PubMed:10601260,
FT ECO:0000269|PubMed:1544921"
FT MOD_RES 43
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MOD_RES 181
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 185
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 187
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT CROSSLNK 176
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT CONFLICT 14
FT /note="L -> H (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 198 AA; 22249 MW; 959CFEC64DAF2F83 CRC64;
MSQPVVVIDA KDHLLGRLAS TIAKQVLNGQ KIVVVRAEAL NISGEFFRNK LKYHDFLRKA
TAFNKTRGPF HFRAPSRILY KAIRGMVSHK TARGKAALER LKIFEGIPPP YDKKKRVVVP
QALRVLRLKP GRKYTTLGKL STSVGWKYED VVAKLEDKRK VRSAEYYAKK RAFTKKVSSA
SAAASESDVA KQLASFGY
