DEF1_YEAST
ID DEF1_YEAST Reviewed; 738 AA.
AC P35732; D6VXN3;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=RNA polymerase II degradation factor 1;
DE AltName: Full=RRM3-interacting protein 1;
GN Name=DEF1; Synonyms=RIP1, VID31; OrderedLocusNames=YKL054C;
GN ORFNames=YKL308;
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].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091862; DOI=10.1002/yea.320100008;
RA Rasmussen S.W.;
RT "Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and
RT TOA2 genes, an open reading frame (ORF) similar to a translationally
RT controlled tumour protein, one ORF containing motifs also found in plant
RT storage proteins and 13 ORFs with weak or no homology to known proteins.";
RL Yeast 10:S63-S68(1994).
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 INTERACTION WITH RAD26, AND FUNCTION.
RX PubMed=11859374; DOI=10.1038/415929a;
RA Woudstra E.C., Gilbert C., Fellows J., Jansen L., Brouwer J.,
RA Erdjument-Bromage H., Tempst P., Svejstrup J.Q.;
RT "A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in
RT response to DNA damage.";
RL Nature 415:929-933(2002).
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 INTERACTION WITH RNA POLYMERASE II, AND FUNCTION.
RX PubMed=15166235; DOI=10.1074/jbc.c400185200;
RA Reid J., Svejstrup J.Q.;
RT "DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement
RT for polymerase ubiquitylation in vitro.";
RL J. Biol. Chem. 279:29875-29878(2004).
RN [7]
RP FUNCTION.
RX PubMed=15960978; DOI=10.1016/j.cell.2005.04.010;
RA Somesh B.P., Reid J., Liu W.F., Sogaard T.M., Erdjument-Bromage H.,
RA Tempst P., Svejstrup J.Q.;
RT "Multiple mechanisms confining RNA polymerase II ubiquitylation to
RT polymerases undergoing transcriptional arrest.";
RL Cell 121:913-923(2005).
RN [8]
RP INTERACTION WITH RRM3, SUBCELLULAR LOCATION, DNA-BINDING, FUNCTION, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15863512; DOI=10.1074/jbc.m413562200;
RA Chen Y.B., Yang C.P., Li R.X., Zeng R., Zhou J.Q.;
RT "Def1p is involved in telomere maintenance in budding yeast.";
RL J. Biol. Chem. 280:24784-24791(2005).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-646, AND
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-273, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; THR-338 AND SER-646, AND
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 [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; SER-307 AND SER-646, AND
RP IDENTIFICATION 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 insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: RNA polymerase II degradation factor recruits the
CC ubiquitination machinery to the RNA polymerase II for
CC polyubiquitination, removal and degradation, when RAD26 fails to
CC efficiently displace stalled RNA polymerase II. Also involved in
CC telomere length regulation. {ECO:0000269|PubMed:11859374,
CC ECO:0000269|PubMed:15166235, ECO:0000269|PubMed:15863512,
CC ECO:0000269|PubMed:15960978}.
CC -!- SUBUNIT: Interacts with the RNA polymerase II in a DNA-damaged
CC dependent manner. Interacts with RAD26. Binds DNA.
CC {ECO:0000269|PubMed:11859374, ECO:0000269|PubMed:15166235,
CC ECO:0000269|PubMed:15863512}.
CC -!- INTERACTION:
CC P35732; P40352: RAD26; NbExp=2; IntAct=EBI-26695, EBI-14687;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15863512}.
CC Chromosome, telomere {ECO:0000269|PubMed:15863512}.
CC -!- MISCELLANEOUS: Present with 3380 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DEF1 family. {ECO:0000305}.
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DR EMBL; X75781; CAA53418.1; -; Genomic_DNA.
DR EMBL; Z28054; CAA81890.1; -; Genomic_DNA.
DR EMBL; BK006944; DAA09103.1; -; Genomic_DNA.
DR PIR; S37876; S37876.
DR RefSeq; NP_012869.1; NM_001179620.1.
DR AlphaFoldDB; P35732; -.
DR SMR; P35732; -.
DR BioGRID; 34079; 413.
DR ComplexPortal; CPX-1189; RAD26-DEF1 stalled RNAPII response complex.
DR DIP; DIP-6354N; -.
DR IntAct; P35732; 45.
DR MINT; P35732; -.
DR STRING; 4932.YKL054C; -.
DR iPTMnet; P35732; -.
DR MaxQB; P35732; -.
DR PaxDb; P35732; -.
DR PRIDE; P35732; -.
DR EnsemblFungi; YKL054C_mRNA; YKL054C; YKL054C.
DR GeneID; 853811; -.
DR KEGG; sce:YKL054C; -.
DR SGD; S000001537; DEF1.
DR VEuPathDB; FungiDB:YKL054C; -.
DR eggNOG; ENOG502S359; Eukaryota.
DR HOGENOM; CLU_023119_0_0_1; -.
DR InParanoid; P35732; -.
DR OMA; QPEAPYF; -.
DR BioCyc; YEAST:G3O-31854-MON; -.
DR PRO; PR:P35732; -.
DR Proteomes; UP000002311; Chromosome XI.
DR RNAct; P35732; protein.
DR GO; GO:0000785; C:chromatin; IDA:ComplexPortal.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IMP:SGD.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0043130; F:ubiquitin binding; IEA:InterPro.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IMP:SGD.
DR GO; GO:0016567; P:protein ubiquitination; IMP:SGD.
DR GO; GO:0061635; P:regulation of protein complex stability; IDA:ComplexPortal.
DR GO; GO:2001020; P:regulation of response to DNA damage stimulus; IDA:ComplexPortal.
DR GO; GO:0000723; P:telomere maintenance; IMP:SGD.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IGI:SGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:SGD.
DR CDD; cd14368; CUE_DEF1_like; 1.
DR InterPro; IPR003892; CUE.
DR InterPro; IPR041803; DEF1_CUE.
DR Pfam; PF02845; CUE; 1.
DR PROSITE; PS51140; CUE; 1.
PE 1: Evidence at protein level;
KW Chromosome; DNA damage; DNA repair; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Telomere; Ubl conjugation pathway.
FT CHAIN 1..738
FT /note="RNA polymerase II degradation factor 1"
FT /id="PRO_0000203177"
FT DOMAIN 21..63
FT /note="CUE"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00468"
FT REGION 69..455
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 467..503
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 640..688
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..86
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 87..129
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 194..223
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 224..242
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 256..295
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 296..321
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 322..336
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 372..394
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 401..455
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 260
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 273
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MOD_RES 307
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 338
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 646
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
SQ SEQUENCE 738 AA; 83973 MW; 05734E2D0B7389AC CRC64;
MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD LETIIDKITS
GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI TYKSSNNSNS FTSTKHNSSN
NYTQARNKKK VQTPRAHTTG KHVNLDKGKH VPSKPVSNTT SWAAAVSVDT KHDVPQDSND
NNNEELEAQG QQAQEKNQEK EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK
KMSWAAIATP KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE
EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA APEEEVTVVE
EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ QPQQPQQQQQ PQQPQQPQQQ
LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ
HPQPQSQQPQ SQQSPQSQKQ GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA
QNNAQTSGNA NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM
PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG VAQHSEDSQQ
KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ FQQQQQQAAA AAAAAAQQGV
PYGYNGYDYN SKNSRGFY
