ID RL40B_YEAST Reviewed; 128 AA. AC P0CH09; D6VVD9; P04838; P14796; P61864; Q6LA96; DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot. DT 10-AUG-2010, sequence version 1. DT 27-MAR-2024, entry version 108. DE RecName: Full=Ubiquitin-ribosomal protein eL40B fusion protein {ECO:0000305}; DE Contains: DE RecName: Full=Ubiquitin; DE Contains: DE RecName: Full=Large ribosomal subunit protein eL40B {ECO:0000303|PubMed:24524803}; DE AltName: Full=60S ribosomal protein L40-B {ECO:0000303|PubMed:9559554}; DE AltName: Full=CEP52; DE Flags: Precursor; GN Name=RPL40B {ECO:0000303|PubMed:9559554}; Synonyms=UBI2; GN OrderedLocusNames=YKR094C; 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=3038523; DOI=10.1002/j.1460-2075.1987.tb02384.x; RA Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.; RT "The yeast ubiquitin genes: a family of natural gene fusions."; RL EMBO J. 6:1429-1439(1987). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=8154186; DOI=10.1002/yea.320091209; RA Bou G., Esteban P.F., Baladron V., Gonzalez G.A., Cantalejo J.G., RA Remacha M.A., Jimenez A., del Rey F., Ballesta J.P.G., Revuelta J.L.; RT "The complete sequence of a 15,820 bp segment of Saccharomyces cerevisiae RT chromosome XI contains the UBI2 and MPL1 genes and three new open reading RT frames."; RL Yeast 9:1349-1354(1993). RN [3] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=8196765; DOI=10.1038/369371a0; RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A., RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., RA Becker I., Mewes H.-W.; RT "Complete DNA sequence of yeast chromosome XI."; RL Nature 369:371-378(1994). RN [4] 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 [5] RP MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63. RX PubMed=7615550; DOI=10.1074/jbc.270.29.17442; RA Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.; RT "A proteolytic pathway that recognizes ubiquitin as a degradation signal."; RL J. Biol. Chem. 270:17442-17456(1995). RN [6] RP MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN. RX PubMed=7862120; DOI=10.1128/mcb.15.3.1265; RA Spence J., Sadis S., Haas A.L., Finley D.; RT "A ubiquitin mutant with specific defects in DNA repair and RT multiubiquitination."; RL Mol. Cell. Biol. 15:1265-1273(1995). RN [7] RP NOMENCLATURE, AND SUBUNIT (L40). 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] (L40). 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] (L40). 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 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 [11] 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 [12] RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93, AND IDENTIFICATION BY MASS RP 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 [13] RP FUNCTION, AND SUBUNIT. RX PubMed=23169626; DOI=10.1073/pnas.1216454109; RA Lee A.S., Burdeinick-Kerr R., Whelan S.P.; RT "A ribosome-specialized translation initiation pathway is required for cap- RT dependent translation of vesicular stomatitis virus mRNAs."; RL Proc. Natl. Acad. Sci. U.S.A. 110:324-329(2013). 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: [Ubiquitin]: Exists either covalently attached to another CC protein, or free (unanchored). When covalently bound, it is conjugated CC to target proteins via an isopeptide bond either as a monomer CC (monoubiquitin), a polymer linked via different Lys residues of the CC ubiquitin (polyubiquitin chains) or a linear polymer linked via the CC initiator Met of the ubiquitin (linear polyubiquitin chains). CC Polyubiquitin chains, when attached to a target protein, have different CC functions depending on the Lys residue of the ubiquitin that is linked: CC Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved CC in ERAD (endoplasmic reticulum-associated degradation) and in cell- CC cycle regulation; Lys-29-linked is involved in lysosomal degradation; CC Lys-33-linked is involved in kinase modification; Lys-48-linked is CC involved in protein degradation via the proteasome; Lys-63-linked is CC involved in endocytosis, and DNA-damage responses. Linear polymer CC chains formed via attachment by the initiator Met lead to cell CC signaling. Ubiquitin is usually conjugated to Lys residues of target CC proteins, however, in rare cases, conjugation to Cys or Ser residues CC has been observed. When polyubiquitin is free (unanchored- CC polyubiquitin), it also has distinct roles, such as in activation of CC protein kinases, and in signaling (By similarity). {ECO:0000250}. CC -!- FUNCTION: [Large ribosomal subunit protein eL40B]: Component of the CC ribosome, a large ribonucleoprotein complex responsible for the CC synthesis of proteins in the cell. The small ribosomal subunit (SSU) CC binds messenger RNAs (mRNAs) and translates the encoded message by CC selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large CC subunit (LSU) contains the ribosomal catalytic site termed the peptidyl CC transferase center (PTC), which catalyzes the formation of peptide CC bonds, thereby polymerizing the amino acids delivered by tRNAs into a CC polypeptide chain. The nascent polypeptides leave the ribosome through CC a tunnel in the LSU and interact with protein factors that function in CC enzymatic processing, targeting, and the membrane insertion of nascent CC chains at the exit of the ribosomal tunnel (PubMed:22096102). eL40 is CC essential for translation of a subset of cellular transcripts, CC including stress response transcripts, such as DDR2 (PubMed:23169626). CC {ECO:0000269|PubMed:23169626, ECO:0000305|PubMed:22096102}. CC -!- SUBUNIT: [Large ribosomal subunit protein eL40B]: Component of the CC large ribosomal subunit (LSU). Mature yeast ribosomes consist of a CC small (40S) and a large (60S) subunit. The 40S small subunit contains 1 CC molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded CC by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, CC 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) CC (PubMed:9559554, PubMed:22096102). {ECO:0000269|PubMed:22096102, CC ECO:0000305|PubMed:9559554}. CC -!- SUBCELLULAR LOCATION: [Ubiquitin]: Cytoplasm {ECO:0000250}. Nucleus CC {ECO:0000250}. CC -!- SUBCELLULAR LOCATION: [Large ribosomal subunit protein eL40B]: CC Cytoplasm {ECO:0000269|PubMed:22096102}. CC -!- MISCELLANEOUS: Ubiquitin is encoded by several different genes. UBI1 CC and UBI2 genes code for a single copy of ubiquitin fused to the CC ribosomal proteins eL40A and eL40B, respectively. UBI3 is a polyprotein CC with one copy of ubiquitin fused to ribosomal protein eS31. UBI4 is a CC polyprotein containing 5 exact head to tail repeats of ubiquitin. CC {ECO:0000305|PubMed:3038523}. CC -!- MISCELLANEOUS: The 60S ribosomal protein L40 is present with 40000 CC molecules/cell in log phase SD medium. {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: In the N-terminal section; belongs to the ubiquitin family. CC {ECO:0000305}. CC -!- SIMILARITY: In the C-terminal section; belongs to the eukaryotic CC ribosomal protein eL40 family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X73541; CAA51949.1; -; Genomic_DNA. DR EMBL; Z28319; CAA82173.1; -; Genomic_DNA. DR EMBL; BK006944; DAA09244.1; -; Genomic_DNA. DR PIR; A29456; A29456. DR RefSeq; NP_012118.1; NM_001179496.1. DR RefSeq; NP_013020.3; NM_001179884.3. DR PDB; 4V91; EM; 3.70 A; m=1-128. DR PDB; 6NZO; EM; 3.80 A; C/G=1-75. DR PDB; 6PX1; EM; 3.30 A; C/G=1-75. DR PDB; 6PX3; EM; 4.10 A; C/G=1-75. DR PDBsum; 4V91; -. DR PDBsum; 6NZO; -. DR PDBsum; 6PX1; -. DR PDBsum; 6PX3; -. DR AlphaFoldDB; P0CH09; -. DR EMDB; EMD-0559; -. DR EMDB; EMD-20516; -. DR EMDB; EMD-20517; -. DR SMR; P0CH09; -. DR BioGRID; 34225; 394. DR BioGRID; 34844; 220. DR iPTMnet; P0CH09; -. DR TopDownProteomics; P0CH09; -. DR EnsemblFungi; YIL148W_mRNA; YIL148W; YIL148W. DR EnsemblFungi; YKR094C_mRNA; YKR094C; YKR094C. DR GeneID; 853969; -. DR GeneID; 854658; -. DR KEGG; sce:YIL148W; -. DR KEGG; sce:YKR094C; -. DR AGR; SGD:S000001802; -. DR SGD; S000001802; RPL40B. DR VEuPathDB; FungiDB:YIL148W; -. DR VEuPathDB; FungiDB:YKR094C; -. DR GeneTree; ENSGT00940000153593; -. DR HOGENOM; CLU_010412_3_4_1; -. DR InParanoid; P0CH09; -. DR OMA; ARKYKCD; -. DR OrthoDB; 312211at2759; -. DR BioCyc; YEAST:G3O-32057-MONOMER; -. DR BioGRID-ORCS; 853969; 0 hits in 10 CRISPR screens. DR BioGRID-ORCS; 854658; 1 hit in 10 CRISPR screens. DR PRO; PR:P0CH09; -. DR Proteomes; UP000002311; Chromosome XI. DR RNAct; P0CH09; Protein. DR ExpressionAtlas; P0CH09; 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:0005739; C:mitochondrion; HDA:SGD. DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell. DR GO; GO:0031386; F:protein tag activity; ISS:SGD. DR GO; GO:0003735; F:structural constituent of ribosome; IC:SGD. DR GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central. DR GO; GO:0002181; P:cytoplasmic translation; IC:SGD. DR GO; GO:0019941; P:modification-dependent protein catabolic process; IBA:GO_Central. DR GO; GO:0016567; P:protein ubiquitination; IMP:SGD. DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD. DR GO; GO:0000055; P:ribosomal large subunit export from nucleus; IMP:SGD. DR GO; GO:0042254; P:ribosome biogenesis; IDA:SGD. DR CDD; cd01803; Ubl_ubiquitin; 1. DR Gene3D; 4.10.1060.50; -; 1. DR InterPro; IPR001975; Ribosomal_eL40_dom. DR InterPro; IPR038587; Ribosomal_eL40_sf. DR InterPro; IPR000626; Ubiquitin-like_dom. DR InterPro; IPR029071; Ubiquitin-like_domsf. DR InterPro; IPR019954; Ubiquitin_CS. DR InterPro; IPR019956; Ubiquitin_dom. DR PANTHER; PTHR10666; UBIQUITIN; 1. DR Pfam; PF01020; Ribosomal_L40e; 1. DR Pfam; PF00240; ubiquitin; 1. DR PRINTS; PR00348; UBIQUITIN. DR SMART; SM01377; Ribosomal_L40e; 1. DR SMART; SM00213; UBQ; 1. DR SUPFAM; SSF54236; Ubiquitin-like; 1. DR PROSITE; PS00299; UBIQUITIN_1; 1. DR PROSITE; PS50053; UBIQUITIN_2; 1. DR SWISS-2DPAGE; P61864; -. PE 1: Evidence at protein level; KW 3D-structure; Cytoplasm; Isopeptide bond; Nucleus; Reference proteome; KW Ribonucleoprotein; Ribosomal protein; Ubl conjugation. FT CHAIN 1..76 FT /note="Ubiquitin" FT /id="PRO_0000396455" FT CHAIN 77..128 FT /note="Large ribosomal subunit protein eL40B" FT /id="PRO_0000396456" FT DOMAIN 1..76 FT /note="Ubiquitin-like" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214" FT CROSSLNK 76 FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with FT K-? in acceptor proteins)" FT CROSSLNK 93 FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with FT G-Cter in ubiquitin)" FT /evidence="ECO:0007744|PubMed:22106047" FT MUTAGEN 29 FT /note="K->R: Deficiency in ubiquitin-protein conjugate FT formation." FT /evidence="ECO:0000269|PubMed:7615550" FT MUTAGEN 48 FT /note="K->R: Deficiency in ubiquitin-protein conjugate FT formation." FT /evidence="ECO:0000269|PubMed:7615550" FT MUTAGEN 63 FT /note="K->R: Deficiency in ubiquitin-protein conjugate FT formation. Loss of DNA repair function." FT /evidence="ECO:0000269|PubMed:7615550" SQ SEQUENCE 128 AA; 14554 MW; 84BD137A4B1F7797 CRC64; MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY ARLPPRATNC RKRKCGHTNQ LRPKKKLK //