RL4B_YEAST
ID RL4B_YEAST Reviewed; 362 AA.
AC P49626; D6VRZ8;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=60S ribosomal protein L4-B {ECO:0000303|PubMed:9559554};
DE AltName: Full=L2;
DE AltName: Full=Large ribosomal subunit protein uL4-B {ECO:0000303|PubMed:24524803};
DE AltName: Full=RP2;
DE AltName: Full=YL2;
GN Name=RPL4B {ECO:0000303|PubMed:9559554}; Synonyms=RPL2B;
GN OrderedLocusNames=YDR012W; ORFNames=YD8119.17;
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].
RX PubMed=8896275;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b<1085::aid-yea9>3.3.co;2-s;
RA Eide L.G., Sander C., Prydz H.;
RT "Sequencing and analysis of a 35.4 kb region on the right arm of chromosome
RT IV from Saccharomyces cerevisiae reveal 23 open reading frames.";
RL Yeast 12:1085-1090(1996).
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 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]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-200.
RX PubMed=3062369; DOI=10.1128/mcb.8.11.4792-4798.1988;
RA Lucioli A., Presutti C., Ciafre S., Caffarelli E., Fragapane P.,
RA Bozzoni I.;
RT "Gene dosage alteration of L2 ribosomal protein genes in Saccharomyces
RT cerevisiae: effects on ribosome synthesis.";
RL Mol. Cell. Biol. 8:4792-4798(1988).
RN [6]
RP PROTEIN SEQUENCE OF 2-21, 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 [7]
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 [8]
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 [9]
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 [10]
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).
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 SUBUNIT, INTERACTION WITH ACL4 AND KAP104, DOMAIN, SUBCELLULAR LOCATION,
RP AND MUTAGENESIS OF ARG-95; ARG-98; ILE-289; ILE-290; ILE-295; LYS-314;
RP LYS-315; LYS-319; LYS-332 AND PHE-334.
RX PubMed=25936803; DOI=10.1016/j.molcel.2015.03.029;
RA Stelter P., Huber F.M., Kunze R., Flemming D., Hoelz A., Hurt E.;
RT "Coordinated ribosomal L4 protein assembly into the pre-ribosome is
RT regulated by its eukaryote-specific extension.";
RL Mol. Cell 58:854-862(2015).
RN [13]
RP METHYLATION AT ARG-95.
RX PubMed=26046779; DOI=10.1002/pmic.201500032;
RA Plank M., Fischer R., Geoghegan V., Charles P.D., Konietzny R., Acuto O.,
RA Pears C., Schofield C.J., Kessler B.M.;
RT "Expanding the yeast protein arginine methylome.";
RL Proteomics 15:3232-3243(2015).
RN [14]
RP 3D-STRUCTURE MODELING, AND ELECTRON MICROSCOPY.
RX PubMed=14976550; DOI=10.1038/sj.emboj.7600102;
RA Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R.,
RA Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.;
RT "Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome
RT facilitate tRNA translocation.";
RL EMBO J. 23:1008-1019(2004).
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). uL4 is associated with the polypeptide
CC exit tunnel (PubMed:9559554, PubMed:22096102). uL4 interacts with its
CC chaperone ACL4 and the nuclear import receptor KAP104
CC (PubMed:25936803). {ECO:0000269|PubMed:22096102,
CC ECO:0000269|PubMed:25936803, ECO:0000305|PubMed:9559554}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:22096102, ECO:0000269|PubMed:25936803}. Nucleus
CC {ECO:0000269|PubMed:25936803}.
CC -!- DOMAIN: The eukaryote-specific C-terminal extension harbors a nuclear
CC import signal and delivers the ACL4-uL4/RPL4 complex to the pre-
CC ribosome, triggering uL4 release from ACL4 and incorporation into the
CC 60S ribosomal subunit. {ECO:0000269|PubMed:25936803}.
CC -!- PTM: N-terminally acetylated by acetyltransferase NatA.
CC {ECO:0000269|PubMed:1544921}.
CC -!- MISCELLANEOUS: Present with 151000 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- MISCELLANEOUS: There are 2 genes for uL4 in yeast. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL4 family.
CC {ECO:0000305}.
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DR EMBL; X95966; CAA65204.1; -; Genomic_DNA.
DR EMBL; Z48008; CAA88072.1; -; Genomic_DNA.
DR EMBL; Z74308; CAA98832.1; -; Genomic_DNA.
DR EMBL; AY558570; AAS56896.1; -; Genomic_DNA.
DR EMBL; M22583; AAA34975.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11858.1; -; Genomic_DNA.
DR PIR; S50993; S50993.
DR RefSeq; NP_010295.3; NM_001180320.3.
DR PDB; 2WW9; EM; 8.60 A; H=1-362.
DR PDB; 2WWA; EM; 8.90 A; H=1-362.
DR PDB; 2WWB; EM; 6.48 A; H=1-362.
DR PDB; 4V4B; EM; 11.70 A; BD=2-362.
DR PDBsum; 2WW9; -.
DR PDBsum; 2WWA; -.
DR PDBsum; 2WWB; -.
DR PDBsum; 4V4B; -.
DR AlphaFoldDB; P49626; -.
DR SMR; P49626; -.
DR BioGRID; 32063; 222.
DR DIP; DIP-5367N; -.
DR IntAct; P49626; 209.
DR MINT; P49626; -.
DR STRING; 4932.YDR012W; -.
DR iPTMnet; P49626; -.
DR MaxQB; P49626; -.
DR PaxDb; P49626; -.
DR PRIDE; P49626; -.
DR EnsemblFungi; YDR012W_mRNA; YDR012W; YDR012W.
DR GeneID; 851575; -.
DR KEGG; sce:YDR012W; -.
DR SGD; S000002419; RPL4B.
DR VEuPathDB; FungiDB:YDR012W; -.
DR eggNOG; KOG1475; Eukaryota.
DR GeneTree; ENSGT00390000018145; -.
DR HOGENOM; CLU_026535_4_0_1; -.
DR InParanoid; P49626; -.
DR OMA; PCIICNE; -.
DR BioCyc; YEAST:G3O-29631-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 EvolutionaryTrace; P49626; -.
DR PRO; PR:P49626; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P49626; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003723; F:RNA 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 Gene3D; 3.40.1370.10; -; 1.
DR InterPro; IPR025755; Ribos_L4_C_dom.
DR InterPro; IPR002136; Ribosomal_L4/L1e.
DR InterPro; IPR013000; Ribosomal_L4/L1e_euk/arc_CS.
DR InterPro; IPR023574; Ribosomal_L4_dom_sf.
DR InterPro; IPR045240; Ribosomal_L4_euk/arch.
DR PANTHER; PTHR19431; PTHR19431; 1.
DR Pfam; PF14374; Ribos_L4_asso_C; 1.
DR Pfam; PF00573; Ribosomal_L4; 1.
DR SUPFAM; SSF52166; SSF52166; 1.
DR PROSITE; PS00939; RIBOSOMAL_L1E; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing;
KW Methylation; Nucleus; Reference proteome; Ribonucleoprotein;
KW Ribosomal protein; RNA-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1544921"
FT CHAIN 2..362
FT /note="60S ribosomal protein L4-B"
FT /id="PRO_0000129368"
FT REGION 277..362
FT /note="C-terminal-extended nuclear localization signal"
FT /evidence="ECO:0000269|PubMed:25936803"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:1544921"
FT MOD_RES 95
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000269|PubMed:26046779"
FT MUTAGEN 95
FT /note="R->E: Leads to a slower growth at higher
FT temperatures but allows RPL4 assembly into the 60S subunit;
FT when associated with E-98."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 98
FT /note="R->E: Leads to a slower growth at higher
FT temperatures but allows RPL4 assembly into the mature 60S;
FT when associated with E-95."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 289
FT /note="I->A: Leads to an inefficient release from ACL4 with
FT a delayed assembly into the 60S subunit; when associated
FT with A-290 and A-295."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 290
FT /note="I->A: Leads to an inefficient release from ACL4 with
FT a delayed assembly into the 60S subunit; when associated
FT with A-289 and A-295."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 295
FT /note="I->A: Leads to an inefficient release from ACL4 with
FT a delayed assembly into the 60S subunit; when associated
FT with A-289 and A-290."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 314
FT /note="K->A: Significantly diminished nuclear localization;
FT when associated with A-315 and A-319."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 315
FT /note="K->A: Significantly diminished nuclear localization;
FT when associated with A-314 and A-319."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 319
FT /note="K->A: Significantly diminished nuclear localization;
FT when associated with A-314 and A-315."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 332
FT /note="K->E: Leads to an inefficient release from ACL4 with
FT a delayed assembly into the 60S subunit; when associated
FT with A-334."
FT /evidence="ECO:0000269|PubMed:25936803"
FT MUTAGEN 334
FT /note="F->A: Leads to an inefficient release from ACL4 with
FT a delayed assembly into the 60S subunit; when associated
FT with e-332."
FT /evidence="ECO:0000269|PubMed:25936803"
FT CONFLICT 88
FT /note="G -> R (in Ref. 5; AAA34975)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 362 AA; 39062 MW; 37D0942A10AAF4EF CRC64;
MSRPQVTVHS LTGEATANAL PLPAVFSAPI RPDIVHTVFT SVNKNKRQAY AVSEKAGHQT
SAESWGTGRA VARIPRVGGG GTGRSGQGAF GNMCRGGRMF APTKTWRKWN VKVNHNEKRY
ATASAIAATA VASLVLARGH RVEKIPEIPL VVSTDLESIQ KTKEAVAALK AVGAHSDLLK
VLKSKKLRAG KGKYRNRRWT QRRGPLVVYA EDNGIVKALR NVPGVETANV ASLNLLQLAP
GAHLGRFVIW TEAAFTKLDQ VWGSETVASS KVGYTLPSHI ISTSDVTRII NSSEIQSAIR
PAGQATQKRT HVLKKNPLKN KQVLLRLNPY AKVFAAEKLG SKKAEKTGTK PAAVFAETLK
HD
