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Ubiquitin-60S ribosomal protein L40 [Cleaved into: Ubiquitin; 60S ribosomal protein L40-B (CEP52) (Large ribosomal subunit protein eL40-B)]

 RL40B_YEAST             Reviewed;         128 AA.
P0CH09; D6VVD9; P04838; P14796; P61864; Q6LA96;
10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
10-AUG-2010, sequence version 1.
12-SEP-2018, entry version 76.
RecName: Full=Ubiquitin-60S ribosomal protein L40;
Contains:
RecName: Full=Ubiquitin;
Contains:
RecName: Full=60S ribosomal protein L40-B {ECO:0000303|PubMed:9559554};
AltName: Full=CEP52;
AltName: Full=Large ribosomal subunit protein eL40-B {ECO:0000303|PubMed:24524803};
Flags: Precursor;
Name=RPL40B {ECO:0000303|PubMed:9559554}; Synonyms=UBI2;
OrderedLocusNames=YKR094C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3038523;
Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.;
"The yeast ubiquitin genes: a family of natural gene fusions.";
EMBO J. 6:1429-1439(1987).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=8154186; DOI=10.1002/yea.320091209;
Bou G., Esteban P.F., Baladron V., Gonzalez G.A., Cantalejo J.G.,
Remacha M.A., Jimenez A., del Rey F., Ballesta J.P.G., Revuelta J.L.;
"The complete sequence of a 15,820 bp segment of Saccharomyces
cerevisiae chromosome XI contains the UBI2 and MPL1 genes and three
new open reading frames.";
Yeast 9:1349-1354(1993).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8196765; DOI=10.1038/369371a0;
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M.,
Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C.,
Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G.,
Zimmermann J., Haasemann M., Becker I., Mewes H.-W.;
"Complete DNA sequence of yeast chromosome XI.";
Nature 369:371-378(1994).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
PubMed=7615550; DOI=10.1074/jbc.270.29.17442;
Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.;
"A proteolytic pathway that recognizes ubiquitin as a degradation
signal.";
J. Biol. Chem. 270:17442-17456(1995).
[6]
MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN.
PubMed=7862120; DOI=10.1128/MCB.15.3.1265;
Spence J., Sadis S., Haas A.L., Finley D.;
"A ubiquitin mutant with specific defects in DNA repair and
multiubiquitination.";
Mol. Cell. Biol. 15:1265-1273(1995).
[7]
NOMENCLATURE, AND SUBUNIT (L40).
PubMed=9559554;
DOI=10.1002/(SICI)1097-0061(19980330)14:5<471::AID-YEA241>3.0.CO;2-U;
Planta R.J., Mager W.H.;
"The list of cytoplasmic ribosomal proteins of Saccharomyces
cerevisiae.";
Yeast 14:471-477(1998).
[8]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[9]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[10]
SUBUNIT, AND SUBCELLULAR LOCATION.
PubMed=22096102; DOI=10.1126/science.1212642;
Ben-Shem A., Garreau de Loubresse N., Melnikov S., Jenner L.,
Yusupova G., Yusupov M.;
"The structure of the eukaryotic ribosome at 3.0 A resolution.";
Science 334:1524-1529(2011).
[11]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
[12]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-93, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22106047; DOI=10.1002/pmic.201100166;
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
"Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
Proteomics 12:236-240(2012).
[13]
FUNCTION, AND SUBUNIT.
PubMed=23169626; DOI=10.1073/pnas.1216454109;
Lee A.S., Burdeinick-Kerr R., Whelan S.P.;
"A ribosome-specialized translation initiation pathway is required for
cap-dependent translation of vesicular stomatitis virus mRNAs.";
Proc. Natl. Acad. Sci. U.S.A. 110:324-329(2013).
[14]
NOMENCLATURE.
PubMed=24524803; DOI=10.1016/j.sbi.2014.01.002;
Ban N., Beckmann R., Cate J.H.D., Dinman J.D., Dragon F., Ellis S.R.,
Lafontaine D.L.J., Lindahl L., Liljas A., Lipton J.M., McAlear M.A.,
Moore P.B., Noller H.F., Ortega J., Panse V.G., Ramakrishnan V.,
Spahn C.M.T., Steitz T.A., Tchorzewski M., Tollervey D., Warren A.J.,
Williamson J.R., Wilson D., Yonath A., Yusupov M.;
"A new system for naming ribosomal proteins.";
Curr. Opin. Struct. Biol. 24:165-169(2014).
-!- FUNCTION: Ubiquitin: Exists either covalently attached to another
protein, or free (unanchored). When covalently bound, it is
conjugated to target proteins via an isopeptide bond either as a
monomer (monoubiquitin), a polymer linked via different Lys
residues of the ubiquitin (polyubiquitin chains) or a linear
polymer linked via the initiator Met of the ubiquitin (linear
polyubiquitin chains). Polyubiquitin chains, when attached to a
target protein, have different functions depending on the Lys
residue of the ubiquitin that is linked: Lys-6-linked may be
involved in DNA repair; Lys-11-linked is involved in ERAD
(endoplasmic reticulum-associated degradation) and in cell-cycle
regulation; Lys-29-linked is involved in lysosomal degradation;
Lys-33-linked is involved in kinase modification; Lys-48-linked is
involved in protein degradation via the proteasome; Lys-63-linked
is involved in endocytosis, and DNA-damage responses. Linear
polymer chains formed via attachment by the initiator Met lead to
cell signaling. Ubiquitin is usually conjugated to Lys residues of
target proteins, however, in rare cases, conjugation to Cys or Ser
residues has been observed. When polyubiquitin is free
(unanchored-polyubiquitin), it also has distinct roles, such as in
activation of protein kinases, and in signaling (By similarity).
{ECO:0000250}.
-!- FUNCTION: 60S ribosomal protein L40-B: Component of the ribosome,
a large ribonucleoprotein complex responsible for the synthesis of
proteins in the cell. The small ribosomal subunit (SSU) binds
messenger RNAs (mRNAs) and translates the encoded message by
selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The
large subunit (LSU) contains the ribosomal catalytic site termed
the peptidyl transferase center (PTC), which catalyzes the
formation of peptide bonds, thereby polymerizing the amino acids
delivered by tRNAs into a polypeptide chain. The nascent
polypeptides leave the ribosome through a tunnel in the LSU and
interact with protein factors that function in enzymatic
processing, targeting, and the membrane insertion of nascent
chains at the exit of the ribosomal tunnel (PubMed:22096102). eL40
is essential for translation of a subset of cellular transcripts,
including stress response transcripts, such as DDR2
(PubMed:23169626). {ECO:0000269|PubMed:23169626,
ECO:0000305|PubMed:22096102}.
-!- SUBUNIT: Component of the large ribosomal subunit (LSU). Mature
yeast ribosomes consist of a small (40S) and a large (60S)
subunit. The 40S small subunit contains 1 molecule of ribosomal
RNA (18S rRNA) and 33 different proteins (encoded by 57 genes).
The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S
rRNA) and 46 different proteins (encoded by 81 genes)
(PubMed:9559554, PubMed:22096102). {ECO:0000269|PubMed:22096102,
ECO:0000305|PubMed:9559554}.
-!- SUBCELLULAR LOCATION: Ubiquitin: Cytoplasm {ECO:0000250}. Nucleus
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: 60S ribosomal protein L40-B: Cytoplasm
{ECO:0000269|PubMed:22096102}.
-!- MISCELLANEOUS: Ubiquitin is encoded by several different genes.
UBI1 and UBI2 genes code for a single copy of ubiquitin fused to
the ribosomal proteins eL40. UBI3 is a polyprotein with one copy
of ubiquitin fused to ribosomal protein eS31. UBI4 is a
polyprotein containing 5 exact head to tail repeats of ubiquitin.
{ECO:0000305|PubMed:3038523}.
-!- MISCELLANEOUS: The 60S ribosomal protein L40 is present with 40000
molecules/cell in log phase SD medium.
{ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: In the N-terminal section; belongs to the ubiquitin
family. {ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the eukaryotic
ribosomal protein eL40 family. {ECO:0000305}.
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EMBL; X73541; CAA51949.1; -; Genomic_DNA.
EMBL; Z28319; CAA82173.1; -; Genomic_DNA.
EMBL; BK006944; DAA09244.1; -; Genomic_DNA.
PIR; A29456; A29456.
RefSeq; NP_012118.1; NM_001179496.1.
RefSeq; NP_013020.3; NM_001179884.3.
PDB; 4V91; EM; 3.70 A; m=1-128.
PDBsum; 4V91; -.
ProteinModelPortal; P0CH09; -.
SMR; P0CH09; -.
BioGrid; 34225; 375.
BioGrid; 34844; 184.
iPTMnet; P0CH09; -.
SWISS-2DPAGE; P61864; -.
TopDownProteomics; P0CH09; -.
EnsemblFungi; YIL148W; YIL148W; YIL148W.
EnsemblFungi; YKR094C; YKR094C; YKR094C.
GeneID; 853969; -.
GeneID; 854658; -.
KEGG; sce:YIL148W; -.
KEGG; sce:YKR094C; -.
SGD; S000001802; RPL40B.
GeneTree; ENSGT00920000149069; -.
InParanoid; P0CH09; -.
KO; K02927; -.
OrthoDB; EOG092C5P9Y; -.
BioCyc; YEAST:G3O-32057-MONOMER; -.
Reactome; R-SCE-110312; Translesion synthesis by REV1.
Reactome; R-SCE-110314; Recognition of DNA damage by PCNA-containing replication complex.
Reactome; R-SCE-110320; Translesion Synthesis by POLH.
Reactome; R-SCE-156827; L13a-mediated translational silencing of Ceruloplasmin expression.
Reactome; R-SCE-174113; SCF-beta-TrCP mediated degradation of Emi1.
Reactome; R-SCE-1799339; SRP-dependent cotranslational protein targeting to membrane.
Reactome; R-SCE-187577; SCF(Skp2)-mediated degradation of p27/p21.
Reactome; R-SCE-382556; ABC-family proteins mediated transport.
Reactome; R-SCE-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
Reactome; R-SCE-5655862; Translesion synthesis by POLK.
Reactome; R-SCE-5656121; Translesion synthesis by POLI.
Reactome; R-SCE-5656169; Termination of translesion DNA synthesis.
Reactome; R-SCE-5675221; Negative regulation of MAPK pathway.
Reactome; R-SCE-5687128; MAPK6/MAPK4 signaling.
Reactome; R-SCE-5689603; UCH proteinases.
Reactome; R-SCE-5689880; Ub-specific processing proteases.
Reactome; R-SCE-5689901; Metalloprotease DUBs.
Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
Reactome; R-SCE-5696394; DNA Damage Recognition in GG-NER.
Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
Reactome; R-SCE-5696397; Gap-filling DNA repair synthesis and ligation in GG-NER.
Reactome; R-SCE-5696400; Dual Incision in GG-NER.
Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-SCE-6782135; Dual incision in TC-NER.
Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-SCE-68949; Orc1 removal from chromatin.
Reactome; R-SCE-69017; CDK-mediated phosphorylation and removal of Cdc6.
Reactome; R-SCE-69229; Ubiquitin-dependent degradation of Cyclin D1.
Reactome; R-SCE-69601; Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
Reactome; R-SCE-72689; Formation of a pool of free 40S subunits.
Reactome; R-SCE-72706; GTP hydrolysis and joining of the 60S ribosomal subunit.
Reactome; R-SCE-8854050; FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
Reactome; R-SCE-8866652; Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
Reactome; R-SCE-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
Reactome; R-SCE-9033241; Peroxisomal protein import.
Reactome; R-SCE-917937; Iron uptake and transport.
Reactome; R-SCE-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
Reactome; R-SCE-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
PRO; PR:P0CH09; -.
Proteomes; UP000002311; Chromosome XI.
ExpressionAtlas; P0CH09; differential.
GO; GO:0022625; C:cytosolic large ribosomal subunit; IDA:SGD.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0031386; F:protein tag; ISS:SGD.
GO; GO:0003735; F:structural constituent of ribosome; IC:SGD.
GO; GO:0002181; P:cytoplasmic translation; IC:SGD.
GO; GO:0016567; P:protein ubiquitination; IMP:SGD.
GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD.
GO; GO:0000055; P:ribosomal large subunit export from nucleus; IMP:SGD.
GO; GO:0042254; P:ribosome biogenesis; IDA:SGD.
Gene3D; 2.20.28.70; -; 1.
InterPro; IPR038587; L40e_sf.
InterPro; IPR001975; Ribosomal_L40e.
InterPro; IPR019956; Ubiquitin.
InterPro; IPR029071; Ubiquitin-like_domsf.
InterPro; IPR019954; Ubiquitin_CS.
InterPro; IPR000626; Ubiquitin_dom.
Pfam; PF01020; Ribosomal_L40e; 1.
Pfam; PF00240; ubiquitin; 1.
PRINTS; PR00348; UBIQUITIN.
SMART; SM01377; Ribosomal_L40e; 1.
SMART; SM00213; UBQ; 1.
SUPFAM; SSF54236; SSF54236; 1.
PROSITE; PS00299; UBIQUITIN_1; 1.
PROSITE; PS50053; UBIQUITIN_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Isopeptide bond; Nucleus;
Reference proteome; Ribonucleoprotein; Ribosomal protein;
Ubl conjugation.
CHAIN 1 76 Ubiquitin.
/FTId=PRO_0000396455.
CHAIN 77 128 60S ribosomal protein L40-B.
/FTId=PRO_0000396456.
DOMAIN 1 76 Ubiquitin-like. {ECO:0000255|PROSITE-
ProRule:PRU00214}.
CROSSLNK 76 76 Glycyl lysine isopeptide (Gly-Lys)
(interchain with K-? in acceptor
proteins).
CROSSLNK 93 93 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000244|PubMed:22106047}.
MUTAGEN 29 29 K->R: Deficiency in ubiquitin-protein
conjugate formation.
{ECO:0000269|PubMed:7615550}.
MUTAGEN 48 48 K->R: Deficiency in ubiquitin-protein
conjugate formation.
{ECO:0000269|PubMed:7615550}.
MUTAGEN 63 63 K->R: Deficiency in ubiquitin-protein
conjugate formation. Loss of DNA repair
function. {ECO:0000269|PubMed:7615550}.
SEQUENCE 128 AA; 14554 MW; 84BD137A4B1F7797 CRC64;
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN
IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY ARLPPRATNC RKRKCGHTNQ
LRPKKKLK


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