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 02-SEP-2026, entry version 181. 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 FUNCTION, INTERACTION WITH RRM3, SUBCELLULAR LOCATION, AND IDENTIFICATION RP 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). RN [13] RP SUBUNIT, INTERACTION WITH ELA1 AND RPO21, SUBCELLULAR LOCATION, RP UBIQUITINATION, PROTEOLYTIC PROCESSING, IDENTIFICATION BY MASS RP SPECTROMETRY, AND MUTAGENESIS OF 33-PHE-PRO-34 AND 54-ILE-ILE-55. RX PubMed=23993092; DOI=10.1016/j.cell.2013.07.028; RA Wilson M.D., Harreman M., Taschner M., Reid J., Walker J., RA Erdjument-Bromage H., Tempst P., Svejstrup J.Q.; RT "Proteasome-mediated processing of Def1, a critical step in the cellular RT response to transcription stress."; RL Cell 154:983-995(2013). CC -!- FUNCTION: Recruits the ubiquitination machinery to RNA polymerase II CC for polyubiquitination, removal and degradation, when the CC transcription-coupled repair (TCR) factor RAD26 fails to efficiently CC displace stalled RNA polymerase II (PubMed:11859374, PubMed:15166235, CC PubMed:15960978). Also involved in telomere length regulation CC (PubMed:15863512). Binds DNA (PubMed:15863512). CC {ECO:0000269|PubMed:11859374, ECO:0000269|PubMed:15166235, CC ECO:0000269|PubMed:15863512, ECO:0000269|PubMed:15960978}. CC -!- SUBUNIT: Homodimer; may form higher order oligomers (PubMed:23993092). CC Interacts with the large RNA polymerase II subunit RPO21; the CC interaction is direct and serves to bridge RPO21 to the Elongin complex CC in a manner dependent on transcription stress (PubMed:15166235, CC PubMed:23993092). Interacts with RAD26 (PubMed:11859374). Interacts CC (via CUE domain) with the Elongin complex subunit ELA1 (via C- CC terminus); the interaction is direct (PubMed:23993092). CC {ECO:0000269|PubMed:11859374, ECO:0000269|PubMed:15166235, CC ECO:0000269|PubMed:23993092}. CC -!- INTERACTION: CC P35732; P40352: RAD26; NbExp=2; IntAct=EBI-26695, EBI-14687; CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23993092}. Nucleus CC {ECO:0000269|PubMed:15863512, ECO:0000269|PubMed:23993092}. Chromosome, CC telomere {ECO:0000269|PubMed:15863512}. Note=During transcription CC stress, localizes to the nucleus following proteolytic cleavage by the CC proteasome. {ECO:0000269|PubMed:23993092}. CC -!- DOMAIN: The C-terminal part appears to promote nuclear export. CC {ECO:0000269|PubMed:23993092}. CC -!- PTM: Ubiquitinated at Lys-281 or Lys-288, and at Lys-328 or Lys-329. in CC a manner dependent on RSP5; ubiquitination accelerates its proteolytic CC processing by the proteasome. {ECO:0000269|PubMed:23993092}. CC -!- PTM: Proteolytically cleaved by the proteasome in response to CC transcription stress; the resulting N-terminal form constitutes the CC activated nuclear form and the C-terminal portion is degraded. CC {ECO:0000269|PubMed:23993092}. 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}. 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; 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; 492. DR ComplexPortal; CPX-1189; RAD26-DEF1 stalled RNAPII response complex. DR DIP; DIP-6354N; -. DR FunCoup; P35732; 347. DR IntAct; P35732; 48. DR MINT; P35732; -. DR STRING; 4932.YKL054C; -. DR iPTMnet; P35732; -. DR PaxDb; 4932-YKL054C; -. DR PeptideAtlas; P35732; -. DR EnsemblFungi; YKL054C_mRNA; YKL054C; YKL054C. DR GeneID; 853811; -. DR KEGG; sce:YKL054C; -. DR AGR; SGD:S000001537; -. DR SGD; S000001537; DEF1. DR VEuPathDB; FungiDB:YKL054C; -. DR eggNOG; ENOG502S359; Eukaryota. DR HOGENOM; CLU_023119_0_0_1; -. DR InParanoid; P35732; -. DR OMA; MYQNQFP; -. DR OrthoDB; 5396806at2759; -. DR BioCyc; YEAST:G3O-31854-MONOMER; -. DR BioGRID-ORCS; 853811; 6 hits in 10 CRISPR screens. 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:0005737; C:cytoplasm; IDA:UniProtKB. DR GO; GO:0005829; C:cytosol; IDA:SGD. DR GO; GO:0005634; C:nucleus; IDA:UniProtKB. DR GO; GO:0062058; F:transcription factor TFIIH holo complex binding; IDA:SGD. DR GO; GO:0043130; F:ubiquitin binding; IDA:UniProtKB. DR GO; GO:0140036; F:ubiquitin-modified protein reader activity; IDA:SGD. DR GO; GO:0006974; P:DNA damage response; IDA:ComplexPortal. DR GO; GO:0061157; P:mRNA destabilization; IMP:SGD. DR GO; GO:0060261; P:positive regulation of transcription initiation by RNA polymerase II; IMP:SGD. DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IDA:SGD. DR GO; GO:0016567; P:protein ubiquitination; IMP:SGD. DR GO; GO:0061013; P:regulation of mRNA catabolic process; IDA:SGD. DR GO; GO:0061635; P:regulation of protein complex stability; IDA:ComplexPortal. DR GO; GO:0000723; P:telomere maintenance; IMP: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 PROSITE; PS51140; CUE; 1. PE 1: Evidence at protein level; KW Chromosome; Cytoplasm; DNA damage; DNA repair; DNA-binding; Nucleus; KW Phosphoprotein; Reference proteome; Telomere; Ubl conjugation; KW 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 500..530 FT /note="Contains the proteolytic activation cleavage site" FT /evidence="ECO:0000269|PubMed:23993092" FT REGION 640..688 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 69..84 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 103..121 FT /note="Low complexity" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 211..220 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 224..237 FT /note="Low complexity" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 256..291 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 298..324 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 325..336 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 337..358 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 380..455 FT /note="Low complexity" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 467..498 FT /note="Low complexity" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 660..688 FT /note="Low complexity" 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" FT MUTAGEN 33..34 FT /note="FP->AA: Decreases binding to ubiquitin and FT interaction with ELA1, and decreases polyubiquitination of FT RPO21 during transcription stress; when associated with FT 54-A--A-55." FT /evidence="ECO:0000269|PubMed:23993092" FT MUTAGEN 54..55 FT /note="II->AA: Decreases binding to ubiquitin and FT interaction with ELA1, and decreases polyubiquitination of FT RPO21 during transcription stress; when associated with FT 33-A--A-34." FT /evidence="ECO:0000269|PubMed:23993092" 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 //