UFD1_YEAST
ID UFD1_YEAST Reviewed; 361 AA.
AC P53044; D6VUI5; Q45U36;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Ubiquitin fusion degradation protein 1;
DE Short=UB fusion protein 1;
DE AltName: Full=Polymerase-interacting protein 3;
GN Name=UFD1; Synonyms=PIP3; OrderedLocusNames=YGR048W;
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], AND MUTAGENESIS OF VAL-94.
RC STRAIN=ATCC 204508 / S288c;
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 [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 200060 / W303;
RX PubMed=9236779; DOI=10.1007/s004380050491;
RA del Olmo M., Mizrahi N., Gross S., Moore C.L.;
RT "The Uba2 and Ufd1 proteins of Saccharomyces cerevisiae interact with
RT poly(A) polymerase and affect the polyadenylation activity of cell
RT extracts.";
RL Mol. Gen. Genet. 255:209-218(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=SK1;
RX PubMed=16273108; DOI=10.1038/ng1674;
RA Deutschbauer A.M., Davis R.W.;
RT "Quantitative trait loci mapped to single-nucleotide resolution in yeast.";
RL Nat. Genet. 37:1333-1340(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [5]
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 [6]
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 [7]
RP FUNCTION, INTERACTION WITH NPL4, AND SUBCELLULAR LOCATION.
RX PubMed=11733065; DOI=10.1016/s0092-8674(01)00595-5;
RA Rape M., Hoppe T., Gorr I., Kalocay M., Richly H., Jentsch S.;
RT "Mobilization of processed, membrane-tethered SPT23 transcription factor by
RT CDC48(UFD1/NPL4), a ubiquitin-selective chaperone.";
RL Cell 107:667-677(2001).
RN [8]
RP INTERACTION WITH NPL4.
RX PubMed=11598205; DOI=10.1091/mbc.12.10.3226;
RA Hitchcock A.L., Krebber H., Frietze S., Lin A., Latterich M., Silver P.A.;
RT "The conserved npl4 protein complex mediates proteasome-dependent membrane-
RT bound transcription factor activation.";
RL Mol. Biol. Cell 12:3226-3241(2001).
RN [9]
RP FUNCTION.
RX PubMed=11740563; DOI=10.1038/414652a;
RA Ye Y., Meyer H.H., Rapoport T.A.;
RT "The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER
RT into the cytosol.";
RL Nature 414:652-656(2001).
RN [10]
RP FUNCTION.
RX PubMed=11847109; DOI=10.1093/emboj/21.4.615;
RA Braun S., Matuschewski K., Rape M., Thoms S., Jentsch S.;
RT "Role of the ubiquitin-selective CDC48(UFD1/NPL4) chaperone (segregase) in
RT ERAD of OLE1 and other substrates.";
RL EMBO J. 21:615-621(2002).
RN [11]
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 [12]
RP IDENTIFICATION IN CDC48-NPL4-UFD1 ATPASE COMPLEX, AND INTERACTION WITH HRD1
RP COMPLEX.
RX PubMed=16873066; DOI=10.1016/j.cell.2006.05.043;
RA Carvalho P., Goder V., Rapoport T.A.;
RT "Distinct ubiquitin-ligase complexes define convergent pathways for the
RT degradation of ER proteins.";
RL Cell 126:361-373(2006).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [16]
RP STRUCTURE BY NMR OF 1-208, FUNCTION, AND UBIQUITINATION.
RX PubMed=16004872; DOI=10.1016/j.str.2005.04.013;
RA Park S., Isaacson R., Kim H.T., Silver P.A., Wagner G.;
RT "Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction
RT sites.";
RL Structure 13:995-1005(2005).
RN [17]
RP IDENTIFICATION IN A COMPLEX WITH NPL4; DOA1; CDC48; OTU1 AND SHP1.
RX PubMed=16427015; DOI=10.1016/j.molcel.2005.12.014;
RA Rumpf S., Jentsch S.;
RT "Functional division of substrate processing cofactors of the ubiquitin-
RT selective Cdc48 chaperone.";
RL Mol. Cell 21:261-269(2006).
CC -!- FUNCTION: Functions at a post-ubiquitation step in the ubiquitin fusion
CC degradation (UFD) pathway. Has a role in the endoplasmic reticulum-
CC associated degradation (ERAD) pathway. Required for the proteasome-
CC dependent processing/activation of MGA2 and SPT23 transcription factors
CC leading to the subsequent expression of OLE1. Has an additional role in
CC the turnover of OLE1 where it targets ubiquitinated OLE1 and other
CC proteins to the ERAD. {ECO:0000269|PubMed:11733065,
CC ECO:0000269|PubMed:11740563, ECO:0000269|PubMed:11847109,
CC ECO:0000269|PubMed:16004872}.
CC -!- SUBUNIT: Component of the heterotrimeric CDC48-NPL4-UFD1 ATPase complex
CC (PubMed:16873066). The CDC48-NPL4-UFD1 ATPase complex interacts with
CC the HRD1 ubiquitin ligase complex composed of the E3 ligase HRD1, its
CC cofactors HRD3, USA1 and DER1, substrate recruiting factor YOS9 and
CC CDC48-binding protein UBX2 (PubMed:16873066). Interaction between the
CC complexes is mediated by interaction between CDC48-NPL4-UFD1 complex
CC member CDC48 and HRD1 complex member UBX2 (PubMed:16873066). Forms a
CC complex composed of CDC48, NPL4, UFD1, DOA1, SHP1 and deubiquitinase
CC OTU1 (PubMed:16427015). Interacts with NPL4, CDC48 AND UBX2
CC (PubMed:11733065, PubMed:11598205, PubMed:16873066).
CC {ECO:0000269|PubMed:11598205, ECO:0000269|PubMed:11733065,
CC ECO:0000269|PubMed:16427015, ECO:0000269|PubMed:16873066}.
CC -!- INTERACTION:
CC P53044; P25694: CDC48; NbExp=13; IntAct=EBI-19997, EBI-4308;
CC P53044; P38307: DER1; NbExp=3; IntAct=EBI-19997, EBI-5761;
CC P53044; P33755: NPL4; NbExp=11; IntAct=EBI-19997, EBI-12193;
CC P53044; P06778: RAD52; NbExp=4; IntAct=EBI-19997, EBI-14719;
CC P53044; Q12306: SMT3; NbExp=3; IntAct=EBI-19997, EBI-17490;
CC P53044; Q04228: UBX2; NbExp=5; IntAct=EBI-19997, EBI-27730;
CC -!- MISCELLANEOUS: Present with 3530 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the UFD1 family. {ECO:0000305}.
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DR EMBL; U22153; AAC49023.1; -; Genomic_DNA.
DR EMBL; U17264; AAB46627.1; -; Genomic_DNA.
DR EMBL; DQ115391; AAZ22463.1; -; Genomic_DNA.
DR EMBL; Z72833; CAA97047.1; -; Genomic_DNA.
DR EMBL; AY692806; AAT92825.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08146.1; -; Genomic_DNA.
DR PIR; S59814; S59814.
DR RefSeq; NP_011562.1; NM_001181177.1.
DR PDB; 1ZC1; NMR; -; A=1-208.
DR PDB; 6JWJ; X-ray; 1.58 A; C=288-305.
DR PDBsum; 1ZC1; -.
DR PDBsum; 6JWJ; -.
DR AlphaFoldDB; P53044; -.
DR BMRB; P53044; -.
DR SMR; P53044; -.
DR BioGRID; 33295; 197.
DR ComplexPortal; CPX-2946; CDC48-NPL4-UFD1 AAA ATPase complex.
DR ComplexPortal; CPX-3265; Ribosome quality control complex.
DR DIP; DIP-1476N; -.
DR IntAct; P53044; 19.
DR MINT; P53044; -.
DR STRING; 4932.YGR048W; -.
DR CarbonylDB; P53044; -.
DR iPTMnet; P53044; -.
DR MaxQB; P53044; -.
DR PaxDb; P53044; -.
DR PRIDE; P53044; -.
DR EnsemblFungi; YGR048W_mRNA; YGR048W; YGR048W.
DR GeneID; 852939; -.
DR KEGG; sce:YGR048W; -.
DR SGD; S000003280; UFD1.
DR VEuPathDB; FungiDB:YGR048W; -.
DR eggNOG; KOG1816; Eukaryota.
DR GeneTree; ENSGT00390000002408; -.
DR HOGENOM; CLU_037790_1_0_1; -.
DR InParanoid; P53044; -.
DR OMA; VCMIETD; -.
DR BioCyc; YEAST:G3O-30766-MON; -.
DR Reactome; R-SCE-110320; Translesion Synthesis by POLH.
DR Reactome; R-SCE-8951664; Neddylation.
DR Reactome; R-SCE-9755511; KEAP1-NFE2L2 pathway.
DR EvolutionaryTrace; P53044; -.
DR PRO; PR:P53044; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53044; protein.
DR GO; GO:0005829; C:cytosol; HDA:SGD.
DR GO; GO:0000837; C:Doa10p ubiquitin ligase complex; IDA:SGD.
DR GO; GO:0000839; C:Hrd1p ubiquitin ligase ERAD-L complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0030894; C:replisome; IDA:SGD.
DR GO; GO:1990112; C:RQC complex; IDA:SGD.
DR GO; GO:0034098; C:VCP-NPL4-UFD1 AAA ATPase complex; IDA:SGD.
DR GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; IDA:SGD.
DR GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
DR GO; GO:0071629; P:cytoplasm protein quality control by the ubiquitin-proteasome system; IMP:SGD.
DR GO; GO:0006274; P:DNA replication termination; IDA:SGD.
DR GO; GO:0071712; P:ER-associated misfolded protein catabolic process; IDA:ComplexPortal.
DR GO; GO:0072671; P:mitochondria-associated ubiquitin-dependent protein catabolic process; IMP:UniProtKB.
DR GO; GO:0051974; P:negative regulation of telomerase activity; IMP:SGD.
DR GO; GO:0070651; P:nonfunctional rRNA decay; IMP:SGD.
DR GO; GO:1900182; P:positive regulation of protein localization to nucleus; IMP:SGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR GO; GO:0072665; P:protein localization to vacuole; IMP:SGD.
DR GO; GO:0030970; P:retrograde protein transport, ER to cytosol; IMP:SGD.
DR GO; GO:1990116; P:ribosome-associated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IDA:ComplexPortal.
DR Gene3D; 2.40.40.50; -; 1.
DR IDEAL; IID50028; -.
DR InterPro; IPR004854; Ufd1-like.
DR InterPro; IPR042299; Ufd1-like_Nn.
DR PANTHER; PTHR12555; PTHR12555; 1.
DR Pfam; PF03152; UFD1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Phosphoprotein; Reference proteome; Ubl conjugation pathway.
FT CHAIN 1..361
FT /note="Ubiquitin fusion degradation protein 1"
FT /id="PRO_0000194989"
FT REGION 27..28
FT /note="Monoubiquitin-binding"
FT REGION 30..32
FT /note="Monoubiquitin-binding"
FT REGION 99..101
FT /note="Monoubiquitin-binding"
FT REGION 310..361
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 318..333
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 336..361
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 37
FT /note="Monoubiquitin-binding"
FT SITE 39
FT /note="Monoubiquitin-binding"
FT SITE 109
FT /note="Monoubiquitin-binding"
FT MOD_RES 354
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MUTAGEN 94
FT /note="V->D: In UFD1-1; grows more slowly."
FT /evidence="ECO:0000269|PubMed:7615550"
FT STRAND 19..29
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 30..32
FT /evidence="ECO:0007829|PDB:1ZC1"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 40..44
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 52..60
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:1ZC1"
FT TURN 74..76
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 79..87
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 98..104
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 111..118
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:1ZC1"
FT HELIX 140..150
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 154..164
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 167..177
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:1ZC1"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:6JWJ"
SQ SEQUENCE 361 AA; 39810 MW; 198E0CD48B863B98 CRC64;
MFSGFSSFGG GNGFVNMPQT FEEFFRCYPI AMMNDRIRKD DANFGGKIFL PPSALSKLSM
LNIRYPMLFK LTANETGRVT HGGVLEFIAE EGRVYLPQWM METLGIQPGS LLQISSTDVP
LGQFVKLEPQ SVDFLDISDP KAVLENVLRN FSTLTVDDVI EISYNGKTFK IKILEVKPES
SSKSICVIET DLVTDFAPPV GYVEPDYKAL KAQQDKEKKN SFGKGQVLDP SVLGQGSMST
RIDYAGIANS SRNKLSKFVG QGQNISGKAP KAEPKQDIKD MKITFDGEPA KLDLPEGQLF
FGFPMVLPKE DEESAAGSKS SEQNFQGQGI SLRKSNKRKT KSDHDSSKSK APKSPEVIEI
D
