RL40B_YEAST
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 03-AUG-2022, entry version 99.
DE RecName: Full=Ubiquitin-60S ribosomal protein L40;
DE Contains:
DE RecName: Full=Ubiquitin;
DE Contains:
DE RecName: Full=60S ribosomal protein L40-B {ECO:0000303|PubMed:9559554};
DE AltName: Full=CEP52;
DE AltName: Full=Large ribosomal subunit protein eL40-B {ECO:0000303|PubMed:24524803};
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: [60S ribosomal protein L40-B]: Component of the ribosome, a
CC large ribonucleoprotein complex responsible for the synthesis of
CC proteins in the cell. The small ribosomal subunit (SSU) binds messenger
CC RNAs (mRNAs) and translates the encoded message by selecting cognate
CC aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU)
CC contains the ribosomal catalytic site termed the peptidyl transferase
CC center (PTC), which catalyzes the formation of peptide bonds, thereby
CC polymerizing the amino acids delivered by tRNAs into a polypeptide
CC chain. The nascent polypeptides leave the ribosome through a tunnel in
CC the LSU and interact with protein factors that function in enzymatic
CC processing, targeting, and the membrane insertion of nascent chains at
CC the exit of the ribosomal tunnel (PubMed:22096102). eL40 is essential
CC for translation of a subset of cellular transcripts, including stress
CC response transcripts, such as DDR2 (PubMed:23169626).
CC {ECO:0000269|PubMed:23169626, 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: [Ubiquitin]: Cytoplasm {ECO:0000250}. Nucleus
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [60S ribosomal protein L40-B]: Cytoplasm
CC {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 eL40. UBI3 is a polyprotein with one copy of
CC ubiquitin fused to ribosomal protein eS31. UBI4 is a polyprotein
CC 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}.
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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 SMR; P0CH09; -.
DR BioGRID; 34225; 384.
DR BioGRID; 34844; 193.
DR iPTMnet; P0CH09; -.
DR SWISS-2DPAGE; P61864; -.
DR PRIDE; 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 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; AREYNQN; -.
DR BioCyc; YEAST:G3O-32057-MON; -.
DR Reactome; R-SCE-110312; Translesion synthesis by REV1.
DR Reactome; R-SCE-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-SCE-110320; Translesion Synthesis by POLH.
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-382556; ABC-family proteins mediated transport.
DR Reactome; R-SCE-5358346; Hedgehog ligand biogenesis.
DR Reactome; R-SCE-5655862; Translesion synthesis by POLK.
DR Reactome; R-SCE-5656121; Translesion synthesis by POLI.
DR Reactome; R-SCE-5687128; MAPK6/MAPK4 signaling.
DR Reactome; R-SCE-5689603; UCH proteinases.
DR Reactome; R-SCE-5689880; Ub-specific processing proteases.
DR Reactome; R-SCE-5689901; Metalloprotease DUBs.
DR Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
DR Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-SCE-6782135; Dual incision in TC-NER.
DR Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR Reactome; R-SCE-6804757; Regulation of TP53 Degradation.
DR Reactome; R-SCE-68949; Orc1 removal from chromatin.
DR Reactome; R-SCE-69017; CDK-mediated phosphorylation and removal of Cdc6.
DR Reactome; R-SCE-69541; Stabilization of p53.
DR Reactome; R-SCE-69601; Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
DR Reactome; R-SCE-72689; Formation of a pool of free 40S subunits.
DR Reactome; R-SCE-72695; Formation of the ternary complex, and subsequently, the 43S complex.
DR Reactome; R-SCE-72702; Ribosomal scanning and start codon recognition.
DR Reactome; R-SCE-72706; GTP hydrolysis and joining of the 60S ribosomal subunit.
DR Reactome; R-SCE-75815; Ubiquitin-dependent degradation of Cyclin D.
DR Reactome; R-SCE-8854050; FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
DR Reactome; R-SCE-8866652; Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
DR Reactome; R-SCE-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
DR Reactome; R-SCE-8948747; Regulation of PTEN localization.
DR Reactome; R-SCE-8948751; Regulation of PTEN stability and activity.
DR Reactome; R-SCE-8951664; Neddylation.
DR Reactome; R-SCE-901032; ER Quality Control Compartment (ERQC).
DR Reactome; R-SCE-9020702; Interleukin-1 signaling.
DR Reactome; R-SCE-9033241; Peroxisomal protein import.
DR Reactome; R-SCE-917729; Endosomal Sorting Complex Required For Transport (ESCRT).
DR Reactome; R-SCE-936440; Negative regulators of DDX58/IFIH1 signaling.
DR Reactome; R-SCE-9646399; Aggrephagy.
DR Reactome; R-SCE-9664873; Pexophagy.
DR Reactome; R-SCE-9755511; KEAP1-NFE2L2 pathway.
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 Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR PRO; PR:P0CH09; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P0CH09; protein.
DR ExpressionAtlas; P0CH09; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0031386; F:protein tag; 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 Gene3D; 4.10.1060.50; -; 1.
DR InterPro; IPR038587; L40e_sf.
DR InterPro; IPR001975; Ribosomal_L40e.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR019954; Ubiquitin_CS.
DR InterPro; IPR019956; Ubiquitin_dom.
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; SSF54236; 1.
DR PROSITE; PS00299; UBIQUITIN_1; 1.
DR PROSITE; PS50053; UBIQUITIN_2; 1.
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="60S ribosomal protein L40-B"
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
