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 12-SEP-2018, entry version 155. 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; OC Saccharomycetes; 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 RT 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 RT 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., RA Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., RA Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., RA Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E., RA Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., RA Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., RA Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., RA Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., RA Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., RA Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., RA Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., RA Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., RA Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., RA Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., RA Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., RA Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., RA Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., RA Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., RA Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., RA van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., RA Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., RA Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., RA 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., RA Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and RT 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., RA Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., RA Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., RA Kolodner R.D., LaBaer J.; RT "Approaching a complete repository of sequence-verified protein- RT encoding 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 RT factor by 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., RA Silver P.A.; RT "The conserved npl4 protein complex mediates proteasome-dependent RT membrane-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 RT ER 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 RT (segregase) in 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., RA Dephoure N., 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 THE HRD1 COMPLEX, AND INTERACTION WITH UBX2 AND RP CDC48. 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 RT the degradation of ER proteins."; RL Cell 126:361-373(2006). RN [13] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, AND IDENTIFICATION RP BY 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 RP BY 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 RT phosphoproteome analysis."; RL Mol. Cell. Proteomics 7:1389-1396(2008). RN [15] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, AND IDENTIFICATION RP BY 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 RT insights 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 RT interaction sites."; RL Structure 13:995-1005(2005). CC -!- FUNCTION: Functions at a post-ubiquitation step in the ubiquitin CC fusion degradation (UFD) pathway. Has a role in the endoplasmic CC reticulum-associated degradation (ERAD) pathway. Required for the CC proteasome-dependent processing/activation of MGA2 and SPT23 CC transcription factors leading to the subsequent expression of CC OLE1. Has an additional role in the turnover of OLE1 where it CC targets ubiquitinated OLE1 and other proteins to the ERAD. CC {ECO:0000269|PubMed:11733065, ECO:0000269|PubMed:11740563, CC ECO:0000269|PubMed:11847109, ECO:0000269|PubMed:16004872}. CC -!- SUBUNIT: Component of the HRD1 complex which contains HRD1, HRD3, CC USA1, DER1, YOS9, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is CC composed of the core membrane complex, consisting of the E3 ligase CC HRD1 and its cofactors HRD3, DER1 and USA1, the substrate CC recruiting factor YOS9, and the heterotrimeric UFD1-NPL4-CDC48/p97 CC (UNC) ATPase complex recruited by UBX2/SEL1. Interacts with NPL4, CC CDC48 AND UBX2. {ECO:0000269|PubMed:11598205, CC ECO:0000269|PubMed:11733065, ECO:0000269|PubMed:16873066}. CC -!- INTERACTION: CC P25694:CDC48; NbExp=13; IntAct=EBI-19997, EBI-4308; CC P38307:DER1; NbExp=3; IntAct=EBI-19997, EBI-5761; CC P33755:NPL4; NbExp=11; IntAct=EBI-19997, EBI-12193; CC P06778:RAD52; NbExp=4; IntAct=EBI-19997, EBI-14719; CC Q12306:SMT3; NbExp=3; IntAct=EBI-19997, EBI-17490; CC Q04228:UBX2; NbExp=5; IntAct=EBI-19997, EBI-27730; CC -!- MISCELLANEOUS: Present with 3530 molecules/cell in log phase SD CC medium. {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 PDBsum; 1ZC1; -. DR ProteinModelPortal; P53044; -. DR SMR; P53044; -. DR BioGrid; 33295; 172. DR ComplexPortal; CPX-2946; CDC48-NPL4-UFD1 AAA ATPase complex. DR ComplexPortal; CPX-3265; RQC 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; YGR048W; YGR048W. DR GeneID; 852939; -. DR KEGG; sce:YGR048W; -. DR EuPathDB; FungiDB:YGR048W; -. DR SGD; S000003280; UFD1. DR GeneTree; ENSGT00390000002408; -. DR HOGENOM; HOG000212737; -. DR InParanoid; P53044; -. DR KO; K14016; -. DR OMA; FFGYEIK; -. DR OrthoDB; EOG092C4VXI; -. DR BioCyc; YEAST:G3O-30766-MONOMER; -. DR Reactome; R-SCE-110320; Translesion Synthesis by POLH. DR EvolutionaryTrace; P53044; -. DR PRO; PR:P53044; -. DR Proteomes; UP000002311; Chromosome VII. 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: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:0071712; P:ER-associated misfolded protein catabolic process; IMP:SGD. 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; IMP:SGD. DR InterPro; IPR004854; Ufd1-like. DR PANTHER; PTHR12555; PTHR12555; 1. DR Pfam; PF03152; UFD1; 1. PE 1: Evidence at protein level; KW 3D-structure; Complete proteome; Phosphoprotein; Reference proteome; KW Ubl conjugation pathway. FT CHAIN 1 361 Ubiquitin fusion degradation protein 1. FT /FTId=PRO_0000194989. FT REGION 27 28 Monoubiquitin-binding. FT REGION 30 32 Monoubiquitin-binding. FT REGION 99 101 Monoubiquitin-binding. FT SITE 37 37 Monoubiquitin-binding. FT SITE 39 39 Monoubiquitin-binding. FT SITE 109 109 Monoubiquitin-binding. FT MOD_RES 354 354 Phosphoserine. FT {ECO:0000244|PubMed:17330950, FT ECO:0000244|PubMed:18407956, FT ECO:0000244|PubMed:19779198}. FT MUTAGEN 94 94 V->D: In UFD1-1; grows more slowly. FT {ECO:0000269|PubMed:7615550}. FT STRAND 19 29 {ECO:0000244|PDB:1ZC1}. FT HELIX 30 32 {ECO:0000244|PDB:1ZC1}. FT TURN 35 37 {ECO:0000244|PDB:1ZC1}. FT HELIX 40 44 {ECO:0000244|PDB:1ZC1}. FT STRAND 45 50 {ECO:0000244|PDB:1ZC1}. FT HELIX 52 60 {ECO:0000244|PDB:1ZC1}. FT STRAND 69 72 {ECO:0000244|PDB:1ZC1}. FT TURN 74 76 {ECO:0000244|PDB:1ZC1}. FT STRAND 79 87 {ECO:0000244|PDB:1ZC1}. FT STRAND 93 96 {ECO:0000244|PDB:1ZC1}. FT HELIX 98 104 {ECO:0000244|PDB:1ZC1}. FT STRAND 111 118 {ECO:0000244|PDB:1ZC1}. FT STRAND 123 128 {ECO:0000244|PDB:1ZC1}. FT HELIX 131 135 {ECO:0000244|PDB:1ZC1}. FT HELIX 140 150 {ECO:0000244|PDB:1ZC1}. FT STRAND 154 164 {ECO:0000244|PDB:1ZC1}. FT STRAND 167 177 {ECO:0000244|PDB:1ZC1}. FT STRAND 188 190 {ECO:0000244|PDB:1ZC1}. FT STRAND 192 196 {ECO:0000244|PDB:1ZC1}. 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 //