UFD4_YEAST
ID UFD4_YEAST Reviewed; 1483 AA.
AC P33202; D6VXS6;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=Ubiquitin fusion degradation protein 4;
DE Short=UB fusion protein 4;
DE EC=2.3.2.-;
DE AltName: Full=HECT-type E3 ubiquitin transferase UFD4;
DE EC=2.3.2.26;
GN Name=UFD4; OrderedLocusNames=YKL010C; ORFNames=YKL162;
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=1481574; DOI=10.1002/yea.320081109;
RA Pascolo S., Ghazvini M., Boyer J., Colleaux L., Thierry A., Dujon B.;
RT "The sequence of a 9.3 kb segment located on the left arm of the yeast
RT chromosome XI reveals five open reading frames including the CCE1 gene and
RT putative products related to MYO2 and to the ribosomal protein L10.";
RL Yeast 8:987-995(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8196765; DOI=10.1038/369371a0;
RA Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA Becker I., Mewes H.-W.;
RT "Complete DNA sequence of yeast chromosome XI.";
RL Nature 369:371-378(1994).
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 CHARACTERIZATION.
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 [5]
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 [6]
RP IDENTIFICATION 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 [7]
RP IDENTIFICATION 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 phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-87, 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 [9]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-349, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
CC -!- FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an
CC E2 ubiquitin-conjugating enzyme in the form of a thioester and then
CC directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.26;
CC -!- INTERACTION:
CC P33202; P26188: MGT1; NbExp=2; IntAct=EBI-20010, EBI-10873;
CC P33202; Q01939: RPT6; NbExp=3; IntAct=EBI-20010, EBI-13914;
CC P33202; P54860: UFD2; NbExp=2; IntAct=EBI-20010, EBI-20003;
CC -!- MISCELLANEOUS: A cysteine residue is required for ubiquitin-thioester
CC formation.
CC -!- MISCELLANEOUS: Present with 7380 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the UPL family. K-HECT subfamily. {ECO:0000305}.
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DR EMBL; S53418; AAB24903.1; -; Genomic_DNA.
DR EMBL; Z28010; CAA81845.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09146.1; -; Genomic_DNA.
DR PIR; S30015; S30015.
DR RefSeq; NP_012915.3; NM_001179576.3.
DR AlphaFoldDB; P33202; -.
DR SMR; P33202; -.
DR BioGRID; 34122; 172.
DR DIP; DIP-4873N; -.
DR IntAct; P33202; 30.
DR MINT; P33202; -.
DR STRING; 4932.YKL010C; -.
DR iPTMnet; P33202; -.
DR MaxQB; P33202; -.
DR PaxDb; P33202; -.
DR PRIDE; P33202; -.
DR EnsemblFungi; YKL010C_mRNA; YKL010C; YKL010C.
DR GeneID; 853859; -.
DR KEGG; sce:YKL010C; -.
DR SGD; S000001493; UFD4.
DR VEuPathDB; FungiDB:YKL010C; -.
DR eggNOG; KOG0168; Eukaryota.
DR eggNOG; KOG0170; Eukaryota.
DR GeneTree; ENSGT00940000156517; -.
DR HOGENOM; CLU_000366_1_1_1; -.
DR InParanoid; P33202; -.
DR OMA; FFTIHAQ; -.
DR BioCyc; YEAST:G3O-31819-MON; -.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR PRO; PR:P33202; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P33202; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0016607; C:nuclear speck; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:1904855; F:proteasome regulatory particle binding; IPI:SGD.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:SGD.
DR GO; GO:0010994; P:free ubiquitin chain polymerization; IMP:SGD.
DR GO; GO:0051974; P:negative regulation of telomerase activity; IMP:SGD.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0035519; P:protein K29-linked ubiquitination; IDA:SGD.
DR GO; GO:0000209; P:protein polyubiquitination; IBA:GO_Central.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IMP:SGD.
DR CDD; cd00078; HECTc; 1.
DR Gene3D; 1.25.10.10; -; 1.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR000569; HECT_dom.
DR InterPro; IPR035983; Hect_E3_ubiquitin_ligase.
DR InterPro; IPR045322; HECTD1/TRIP12-like.
DR PANTHER; PTHR45670; PTHR45670; 1.
DR Pfam; PF00632; HECT; 1.
DR SMART; SM00119; HECTc; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
DR SUPFAM; SSF56204; SSF56204; 1.
DR PROSITE; PS50237; HECT; 1.
PE 1: Evidence at protein level;
KW Isopeptide bond; Phosphoprotein; Reference proteome; Transferase;
KW Ubl conjugation; Ubl conjugation pathway.
FT CHAIN 1..1483
FT /note="Ubiquitin fusion degradation protein 4"
FT /id="PRO_0000194998"
FT DOMAIN 1376..1483
FT /note="HECT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00104"
FT REGION 1..117
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1007..1081
FT /note="K-box"
FT COMPBIAS 1..19
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 36..57
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 88..107
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1450
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00104"
FT MOD_RES 87
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT CROSSLNK 349
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
SQ SEQUENCE 1483 AA; 167843 MW; A9B8B9D812C6216F CRC64;
MSENNSHNLD EHESHSENSD YMMDTQVEDD YDEDGHVQGE YSYYPDEDED EHMLSSVGSF
EADDGEDDDN DYHHEDDSGL LYGYHRTQNG SDEDRNEEED GLERSHDNNE FGSNPLHLPD
ILETFAQRLE QRRQTSEGLG QHPVGRTLPE ILSMIGGRME RSAESSARNE RISKLIENTG
NASEDPYIAM ESLKELSENI LMMNQMVVDR IIPMETLIGN IAAILSDKIL REELELQMQA
CRCMYNLFEV CPESISIAVD EHVIPILQGK LVEISYIDLA EQVLETVEYI SRVHGRDILK
TGQLSIYVQF FDFLTIHAQR KAIAIVSNAC SSIRTDDFKT IVEVLPTLKP IFSNATDQPI
LTRLVNAMYG ICGALHGVDK FETLFSLDLI ERIVQLVSIQ DTPLENKLKC LDILTVLAMS
SDVLSRELRE KTDIVDMATR SFQHYSKSPN AGLHETLIYV PNSLLISISR FIVVLFPPED
ERILSADKYT GNSDRGVISN QEKFDSLVQC LIPILVEIYT NAADFDVRRY VLIALLRVVS
CINNSTAKAI NDQLIKLIGS ILAQKETASN ANGTYSSEAG TLLVGGLSLL DLICKKFSEL
FFPSIKREGI FDLVKDLSVD FNNIDLKEDG NENISLSDEE GDLHSSIEEC DEGDEEYDYE
FTDMEIPDSV KPKKISIHIF RTLSLAYIKN KGVNLVNRVL SQMNVEQEAI TEELHQIEGV
VSILENPSTP DKTEEDWKGI WSVLKKCIFH EDFDVSGFEF TSTGLASSIT KRITSSTVSH
FILAKSFLEV FEDCIDRFLE ILQSALTRLE NFSIVDCGLH DGGGVSSLAK EIKIKLVYDG
DASKDNIGTD LSSTIVSVHC IASFTSLNEF LRHRMVRMRF LNSLIPNLTS SSTEADREEE
ENCLDHMRKK NFDFFYDNEK VDMESTVFGV IFNTFVRRNR DLKTLWDDTH TIKFCKSLEG
NNRESEAAEE ANEGKKLRDF YKKREFAQVD TGSSADILTL LDFLHSCGVK SDSFINSKLS
AKLARQLDEP LVVASGALPD WSLFLTRRFP FLFPFDTRML FLQCTSFGYG RLIQLWKNKS
KGSKDLRNDE ALQQLGRITR RKLRISRKTI FATGLKILSK YGSSPDVLEI EYQEEAGTGL
GPTLEFYSVV SKYFARKSLN MWRCNSYSYR SEMDVDTTDD YITTLLFPEP LNPFSNNEKV
IELFGYLGTF VARSLLDNRI LDFRFSKVFF ELLHRMSTPN VTTVPSDVET CLLMIELVDP
LLAKSLKYIV ANKDDNMTLE SLSLTFTVPG NDDIELIPGG CNKSLNSSNV EEYIHGVIDQ
ILGKGIEKQL KAFIEGFSKV FSYERMLILF PDELVDIFGR VEEDWSMATL YTNLNAEHGY
TMDSSIIHDF ISIISAFGKH ERRLFLQFLT GSPKLPIGGF KSLNPKFTVV LKHAEDGLTA
DEYLPSVMTC ANYLKLPKYT SKDIMRSRLC QAIEEGAGAF LLS
