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 24-JAN-2024, entry version 187. 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}. 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; 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 PDB; 8DAR; EM; 3.00 A; H=1-361. DR PDB; 8DAS; EM; 3.50 A; H=1-361. DR PDB; 8DAT; EM; 3.80 A; H=1-361. DR PDB; 8DAU; EM; 3.70 A; H=1-361. DR PDB; 8DAV; EM; 3.50 A; H=1-361. DR PDB; 8DAW; EM; 3.60 A; H=1-361. DR PDBsum; 1ZC1; -. DR PDBsum; 6JWJ; -. DR PDBsum; 8DAR; -. DR PDBsum; 8DAS; -. DR PDBsum; 8DAT; -. DR PDBsum; 8DAU; -. DR PDBsum; 8DAV; -. DR PDBsum; 8DAW; -. DR AlphaFoldDB; P53044; -. DR BMRB; P53044; -. DR SMR; P53044; -. DR BioGRID; 33295; 198. 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; 4932-YGR048W; -. DR PeptideAtlas; P53044; -. DR EnsemblFungi; YGR048W_mRNA; YGR048W; YGR048W. DR GeneID; 852939; -. DR KEGG; sce:YGR048W; -. DR AGR; SGD:S000003280; -. 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 OrthoDB; 1125766at2759; -. DR BioCyc; YEAST:G3O-30766-MONOMER; -. DR Reactome; R-SCE-8951664; Neddylation. DR Reactome; R-SCE-9755511; KEAP1-NFE2L2 pathway. DR BioGRID-ORCS; 852939; 4 hits in 10 CRISPR screens. 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: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:0072344; P:rescue of stalled ribosome; NAS:ComplexPortal. 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; 3.10.330.10; -; 1. DR Gene3D; 2.40.40.50; Ubiquitin fusion degradation protein UFD1, N-terminal domain; 1. DR IDEAL; IID50028; -. DR InterPro; IPR004854; Ufd1-like. DR InterPro; IPR042299; Ufd1-like_Nn. DR PANTHER; PTHR12555; UBIQUITIN FUSION DEGRADATON PROTEIN 1; 1. DR PANTHER; PTHR12555:SF13; UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION PROTEIN 1; 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 TURN 231..234 FT /evidence="ECO:0007829|PDB:8DAR" FT TURN 237..243 FT /evidence="ECO:0007829|PDB:8DAR" FT HELIX 244..252 FT /evidence="ECO:0007829|PDB:8DAR" FT HELIX 254..256 FT /evidence="ECO:0007829|PDB:8DAV" FT STRAND 285..287 FT /evidence="ECO:0007829|PDB:8DAS" 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 //