UBI4P_YEAST
ID UBI4P_YEAST Reviewed; 381 AA.
AC P0CG63; D6VXW7; P04838; P61864; Q6LA96;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=Polyubiquitin {ECO:0000303|PubMed:3038523};
DE Contains:
DE RecName: Full=Ubiquitin;
DE Flags: Precursor;
GN Name=UBI4 {ECO:0000303|PubMed:3038523}; Synonyms=SCD2;
GN OrderedLocusNames=YLL039C {ECO:0000312|SGD:S000003962};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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] OF 191-381.
RX PubMed=6095120; DOI=10.1038/312663a0;
RA Oezkaynak E., Finley D., Varshavsky A.;
RT "The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin
RT precursor protein.";
RL Nature 312:663-666(1984).
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.
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 UBIQUITINATION AT LYS-48 AND GLY-76.
RX PubMed=28757607; DOI=10.1038/s41467-017-00188-1;
RA Matsuo Y., Ikeuchi K., Saeki Y., Iwasaki S., Schmidt C., Udagawa T.,
RA Sato F., Tsuchiya H., Becker T., Tanaka K., Ingolia N.T., Beckmann R.,
RA Inada T.;
RT "Ubiquitination of stalled ribosome triggers ribosome-associated quality
RT control.";
RL Nat. Commun. 8:159-159(2017).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH YUH1.
RX PubMed=10406793; DOI=10.1093/emboj/18.14.3877;
RA Johnston S.C., Riddle S.M., Cohen R.E., Hill C.P.;
RT "Structural basis for the specificity of ubiquitin C-terminal hydrolases.";
RL EMBO J. 18:3877-3887(1999).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH VPS9.
RX PubMed=12628920; DOI=10.1093/emboj/cdg140;
RA Shih S.C., Prag G., Francis S.A., Sutanto M.A., Hurley J.H., Hicke L.;
RT "A ubiquitin-binding motif required for intramolecular monoubiquitylation,
RT the CUE domain.";
RL EMBO J. 22:1273-1281(2003).
RN [10]
RP STRUCTURE BY NMR IN COMPLEX WITH UBC1.
RX PubMed=11591345; DOI=10.1016/s0969-2126(01)00657-8;
RA Hamilton K.S., Ellison M.J., Barber K.R., Williams R.S., Huzil J.T.,
RA McKenna S., Ptak C., Glover M., Shaw G.S.;
RT "Structure of a conjugating enzyme-ubiquitin thiolester intermediate
RT reveals a novel role for the ubiquitin tail.";
RL Structure 9:897-904(2001).
RN [11]
RP STRUCTURE BY NMR OF COMPLEX WITH CUE2 N-TERMINAL DOMAIN.
RX PubMed=12787503; DOI=10.1016/s0092-8674(03)00362-3;
RA Kang R.S., Daniels C.M., Francis S.A., Shih S.C., Salerno W.J., Hicke L.,
RA Radhakrishnan I.;
RT "Solution structure of a CUE-ubiquitin complex reveals a conserved mode of
RT ubiquitin binding.";
RL Cell 113:621-630(2003).
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).
CC {ECO:0000250|UniProtKB:P0CG47}.
CC -!- INTERACTION:
CC P0CG63; P40087: DDI1; NbExp=3; IntAct=EBI-7000452, EBI-5717;
CC P0CG63; P48510: DSK2; NbExp=3; IntAct=EBI-7000452, EBI-6174;
CC P0CG63; P48365: GYP7; NbExp=2; IntAct=EBI-7000452, EBI-8018;
CC P0CG63; P32628: RAD23; NbExp=4; IntAct=EBI-7000452, EBI-14668;
CC P0CG63; P00358: TDH2; NbExp=2; IntAct=EBI-7000452, EBI-7212;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus
CC {ECO:0000250|UniProtKB:Q15843}.
CC -!- MISCELLANEOUS: Ubiquitin is encoded by 4 different genes. UBI1 and UBI2
CC genes code for a single copy of ubiquitin fused to the ribosomal
CC proteins L40. UBI3 is a polyprotein with one copy of ubiquitin fused to
CC ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to
CC tail repeats of ubiquitin.
CC -!- SIMILARITY: Belongs to the ubiquitin family. {ECO:0000305}.
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DR EMBL; X05731; CAA29198.1; -; Genomic_DNA.
DR EMBL; Z73144; CAA97489.1; -; Genomic_DNA.
DR EMBL; X01473; CAA25704.1; -; Genomic_DNA.
DR EMBL; X01474; CAA25706.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09283.1; -; Genomic_DNA.
DR PIR; D29456; UQBY.
DR RefSeq; NP_013061.1; NM_001181859.1.
DR PDB; 1OTR; NMR; -; B=1-76.
DR PDB; 1Q0W; NMR; -; B=1-76.
DR PDB; 1WR1; NMR; -; A=1-76.
DR PDB; 1ZW7; NMR; -; A=1-76.
DR PDB; 2G3Q; NMR; -; B=1-76.
DR PDB; 2JT4; NMR; -; B=1-76.
DR PDB; 2JWZ; NMR; -; A=1-76.
DR PDB; 2KDI; NMR; -; A=2-76.
DR PDB; 2L00; NMR; -; B=1-76.
DR PDB; 3CMM; X-ray; 2.70 A; B/D=1-76.
DR PDB; 3L0W; X-ray; 2.80 A; B=1-76.
DR PDB; 3L10; X-ray; 2.80 A; B=1-76.
DR PDB; 3OLM; X-ray; 2.50 A; D=1-76.
DR PDB; 4HCN; X-ray; 2.60 A; B=1-76.
DR PDB; 4NNJ; X-ray; 2.40 A; B/D/E=305-380.
DR PDB; 4Q5E; X-ray; 1.87 A; B=305-380.
DR PDB; 4Q5H; X-ray; 2.00 A; B=305-380.
DR PDBsum; 1OTR; -.
DR PDBsum; 1Q0W; -.
DR PDBsum; 1WR1; -.
DR PDBsum; 1ZW7; -.
DR PDBsum; 2G3Q; -.
DR PDBsum; 2JT4; -.
DR PDBsum; 2JWZ; -.
DR PDBsum; 2KDI; -.
DR PDBsum; 2L00; -.
DR PDBsum; 3CMM; -.
DR PDBsum; 3L0W; -.
DR PDBsum; 3L10; -.
DR PDBsum; 3OLM; -.
DR PDBsum; 4HCN; -.
DR PDBsum; 4NNJ; -.
DR PDBsum; 4Q5E; -.
DR PDBsum; 4Q5H; -.
DR AlphaFoldDB; P0CG63; -.
DR BMRB; P0CG63; -.
DR SMR; P0CG63; -.
DR BioGRID; 31215; 547.
DR IntAct; P0CG63; 151.
DR MINT; P0CG63; -.
DR STRING; 4932.YLL039C; -.
DR iPTMnet; P0CG63; -.
DR SWISS-2DPAGE; P61864; -.
DR MaxQB; P0CG63; -.
DR PaxDb; P0CG63; -.
DR PRIDE; P0CG63; -.
DR TopDownProteomics; P0CG63; -.
DR EnsemblFungi; YLL039C_mRNA; YLL039C; YLL039C.
DR GeneID; 850620; -.
DR KEGG; sce:YLL039C; -.
DR SGD; S000003962; UBI4.
DR VEuPathDB; FungiDB:YLL039C; -.
DR eggNOG; KOG0001; Eukaryota.
DR GeneTree; ENSGT00940000162439; -.
DR HOGENOM; CLU_010412_7_0_1; -.
DR InParanoid; P0CG63; -.
DR OMA; VHENTRR; -.
DR BioCyc; YEAST:G3O-32141-MON; -.
DR EvolutionaryTrace; P0CG63; -.
DR PRO; PR:P0CG63; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P0CG63; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0031386; F:protein tag; IDA:FlyBase.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central.
DR GO; GO:0019941; P:modification-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0016567; P:protein ubiquitination; IDA:FlyBase.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR019954; Ubiquitin_CS.
DR InterPro; IPR019956; Ubiquitin_dom.
DR Pfam; PF00240; ubiquitin; 5.
DR PRINTS; PR00348; UBIQUITIN.
DR SMART; SM00213; UBQ; 5.
DR SUPFAM; SSF54236; SSF54236; 5.
DR PROSITE; PS00299; UBIQUITIN_1; 5.
DR PROSITE; PS50053; UBIQUITIN_2; 5.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isopeptide bond; Nucleus; Reference proteome;
KW Repeat; Ubl conjugation.
FT CHAIN 1..76
FT /note="Ubiquitin"
FT /id="PRO_0000396306"
FT CHAIN 77..152
FT /note="Ubiquitin"
FT /id="PRO_0000396307"
FT CHAIN 153..228
FT /note="Ubiquitin"
FT /id="PRO_0000396308"
FT CHAIN 229..304
FT /note="Ubiquitin"
FT /id="PRO_0000396309"
FT CHAIN 305..380
FT /note="Ubiquitin"
FT /id="PRO_0000396310"
FT PROPEP 381
FT /id="PRO_0000396311"
FT DOMAIN 1..76
FT /note="Ubiquitin-like 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 77..152
FT /note="Ubiquitin-like 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 153..228
FT /note="Ubiquitin-like 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 229..304
FT /note="Ubiquitin-like 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 305..380
FT /note="Ubiquitin-like 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT CROSSLNK 48
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:7862120"
FT CROSSLNK 76
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
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 ECO:0000269|PubMed:7862120"
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"
FT CONFLICT 352
FT /note="K -> N (in Ref. 4; CAA25706)"
FT /evidence="ECO:0000305"
FT STRAND 231..234
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:1ZW7"
FT HELIX 251..256
FT /evidence="ECO:0007829|PDB:1ZW7"
FT HELIX 266..268
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 274..277
FT /evidence="ECO:0007829|PDB:1ZW7"
FT HELIX 285..287
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:1ZW7"
FT STRAND 306..310
FT /evidence="ECO:0007829|PDB:4Q5E"
FT TURN 312..314
FT /evidence="ECO:0007829|PDB:1Q0W"
FT STRAND 316..320
FT /evidence="ECO:0007829|PDB:4Q5E"
FT STRAND 323..326
FT /evidence="ECO:0007829|PDB:1Q0W"
FT HELIX 327..338
FT /evidence="ECO:0007829|PDB:4Q5E"
FT TURN 342..344
FT /evidence="ECO:0007829|PDB:4Q5E"
FT STRAND 345..349
FT /evidence="ECO:0007829|PDB:4Q5E"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:4NNJ"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:3OLM"
FT HELIX 361..363
FT /evidence="ECO:0007829|PDB:4Q5E"
FT STRAND 370..375
FT /evidence="ECO:0007829|PDB:4Q5E"
FT HELIX 377..379
FT /evidence="ECO:0007829|PDB:2JT4"
SQ SEQUENCE 381 AA; 42826 MW; 68C6235F9909A2AE CRC64;
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN
IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID NVKSKIQDKE GIPPDQQRLI
FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE SSDTIDNVKS
KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT
ITLEVESSDT IDNVKSKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR
LRGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA GKQLEDGRTL
SDYNIQKEST LHLVLRLRGG N
