ID   BYE1_YEAST              Reviewed;         594 AA.
AC   P36106; D6VXT2;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-1994, sequence version 1.
DT   27-MAR-2024, entry version 170.
DE   RecName: Full=Transcription factor BYE1;
DE   AltName: Full=Bypass of ESS1 protein 1;
GN   Name=BYE1; OrderedLocusNames=YKL005C; ORFNames=YKL150;
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 [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   [2]
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   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 90-594.
RX   PubMed=8488728; DOI=10.1002/yea.320090307;
RA   Boyer J., Pascolo S., Richard G.-F., Dujon B.;
RT   "Sequence of a 7.8 kb segment on the left arm of yeast chromosome XI
RT   reveals four open reading frames, including the CAP1 gene, an intron-
RT   containing gene and a gene encoding a homolog to the mammalian UOG-1
RT   gene.";
RL   Yeast 9:279-287(1993).
RN   [4]
RP   FUNCTION, DOMAINS, AND INTERACTION WITH RPB1.
RX   PubMed=14704159; DOI=10.1093/genetics/165.4.1687;
RA   Wu X., Rossettini A., Hanes S.D.;
RT   "The ESS1 prolyl isomerase and its suppressor BYE1 interact with RNA pol II
RT   to inhibit transcription elongation in Saccharomyces cerevisiae.";
RL   Genetics 165:1687-1702(2003).
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   DOMAIN, AND INTERACTION WITH H3K4ME3.
RX   PubMed=17142463; DOI=10.1074/jbc.c600286200;
RA   Shi X., Kachirskaia I., Walter K.L., Kuo J.-H.A., Lake A., Davrazou F.,
RA   Chan S.M., Martin D.G.E., Fingerman I.M., Briggs S.D., Howe L., Utz P.J.,
RA   Kutateladze T.G., Lugovskoy A.A., Bedford M.T., Gozani O.;
RT   "Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD
RT   fingers as novel direct and selective binding modules of histone H3
RT   methylated at either lysine 4 or lysine 36.";
RL   J. Biol. Chem. 282:2450-2455(2007).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-177, 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).
CC   -!- FUNCTION: Negative regulator of transcription elongation.
CC       {ECO:0000269|PubMed:14704159}.
CC   -!- SUBUNIT: Interacts with the RNA polymerase RPB1 subunit and
CC       specifically with the trimethylated H3 histone H3K4me3.
CC       {ECO:0000269|PubMed:14704159, ECO:0000269|PubMed:17142463}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00651}.
CC   -!- DOMAIN: The PHD domain is involved in the binding to H3K4me3.
CC       {ECO:0000269|PubMed:14704159, ECO:0000269|PubMed:17142463}.
CC   -!- MISCELLANEOUS: Present with 892 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the BYE1 family. {ECO:0000305}.
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DR   EMBL; Z28005; CAA81837.1; -; Genomic_DNA.
DR   EMBL; X61398; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; S59773; AAC60551.1; -; Genomic_DNA.
DR   EMBL; BK006944; DAA09152.1; -; Genomic_DNA.
DR   PIR; S37816; S37816.
DR   RefSeq; NP_012921.3; NM_001179571.3.
DR   PDB; 4BXX; X-ray; 3.28 A; X=225-370.
DR   PDB; 4BXZ; X-ray; 4.80 A; X=1-594.
DR   PDB; 4BY1; X-ray; 3.60 A; X=225-370.
DR   PDB; 4BY7; X-ray; 3.15 A; X=225-370.
DR   PDBsum; 4BXX; -.
DR   PDBsum; 4BXZ; -.
DR   PDBsum; 4BY1; -.
DR   PDBsum; 4BY7; -.
DR   AlphaFoldDB; P36106; -.
DR   SMR; P36106; -.
DR   BioGRID; 34128; 114.
DR   MINT; P36106; -.
DR   STRING; 4932.YKL005C; -.
DR   iPTMnet; P36106; -.
DR   MaxQB; P36106; -.
DR   PaxDb; 4932-YKL005C; -.
DR   PeptideAtlas; P36106; -.
DR   EnsemblFungi; YKL005C_mRNA; YKL005C; YKL005C.
DR   GeneID; 853865; -.
DR   KEGG; sce:YKL005C; -.
DR   AGR; SGD:S000001488; -.
DR   SGD; S000001488; BYE1.
DR   VEuPathDB; FungiDB:YKL005C; -.
DR   eggNOG; KOG1634; Eukaryota.
DR   HOGENOM; CLU_495285_0_0_1; -.
DR   InParanoid; P36106; -.
DR   OMA; RTHKGDI; -.
DR   OrthoDB; 5491784at2759; -.
DR   BioCyc; YEAST:G3O-31815-MONOMER; -.
DR   Reactome; R-SCE-6782135; Dual incision in TC-NER.
DR   Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR   BioGRID-ORCS; 853865; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P36106; -.
DR   Proteomes; UP000002311; Chromosome XI.
DR   RNAct; P36106; Protein.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0035064; F:methylated histone binding; IDA:SGD.
DR   GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0006351; P:DNA-templated transcription; IBA:GO_Central.
DR   GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR   CDD; cd15570; PHD_Bye1p_SIZ1_like; 1.
DR   CDD; cd21542; SPOC_Bye1p-like; 1.
DR   DisProt; DP02476; -.
DR   Gene3D; 1.10.472.30; Transcription elongation factor S-II, central domain; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR   InterPro; IPR012921; SPOC_C.
DR   InterPro; IPR003618; TFIIS_cen_dom.
DR   InterPro; IPR036575; TFIIS_cen_dom_sf.
DR   InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR   InterPro; IPR011011; Znf_FYVE_PHD.
DR   InterPro; IPR001965; Znf_PHD.
DR   InterPro; IPR019787; Znf_PHD-finger.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR11477:SF20; PROTEIN PARTNER OF SNF, ISOFORM B; 1.
DR   PANTHER; PTHR11477; TRANSCRIPTION FACTOR S-II ZINC FINGER DOMAIN-CONTAINING PROTEIN; 1.
DR   Pfam; PF00628; PHD; 1.
DR   Pfam; PF07744; SPOC; 1.
DR   Pfam; PF07500; TFIIS_M; 1.
DR   SMART; SM00249; PHD; 1.
DR   SMART; SM00510; TFS2M; 1.
DR   SUPFAM; SSF46942; Elongation factor TFIIS domain 2; 1.
DR   SUPFAM; SSF57903; FYVE/PHD zinc finger; 1.
DR   PROSITE; PS51321; TFIIS_CENTRAL; 1.
DR   PROSITE; PS01359; ZF_PHD_1; 1.
DR   PROSITE; PS50016; ZF_PHD_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Metal-binding; Nucleus; Phosphoprotein; Reference proteome;
KW   Repressor; Transcription; Transcription regulation; Zinc; Zinc-finger.
FT   CHAIN           1..594
FT                   /note="Transcription factor BYE1"
FT                   /id="PRO_0000203191"
FT   DOMAIN          254..365
FT                   /note="TFIIS central"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00651"
FT   ZN_FING         72..134
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          23..65
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          142..231
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        142..193
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        205..231
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         177
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   HELIX           234..251
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           254..258
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           272..283
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           285..289
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           302..314
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   STRAND          317..319
FT                   /evidence="ECO:0007829|PDB:4BXX"
FT   HELIX           320..327
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           332..336
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   HELIX           346..359
FT                   /evidence="ECO:0007829|PDB:4BY7"
FT   TURN            360..362
FT                   /evidence="ECO:0007829|PDB:4BY7"
SQ   SEQUENCE   594 AA;  67901 MW;  1AE16A20E33F21C9 CRC64;
     MSVRTSSRSN KGQNKYIEYL LQEETEAPKK KRTKKKVDSA IEKNKKSDSS QEPRKDTENV
     RTDEVDEADE GYVRCLCGAN NENYDAAEYS HGDMVQCDGC DTWQHIKCMT DGKDTIDGLM
     SEDSKYYCEL CDPSLYAHLE TSKEAEVSED EDYHDDVYKP VNDHDDNDAD VFLDEESPRK
     RKRSPDSAKG IHIKSKQVKK SNGSKKRNKS IDAAKSDTAE NEMPTRKDFE SEKEHKLRYN
     AEKMFSTLFS KFIVPETIEA KLYELPDGKD VISISQEFAH NLEEELYKAC LNVEFGTLDK
     IYTEKVRSLY SNLKDKKNLE LKAHVVEGKL PLNKLVNMNA SELANPDLQE FKEKRDKIIL
     ENFIVEVPDK PMYVKTHKGD ELIEDIAEPQ EDILYSKDSI RLHNIDSIDS DKSKIEQTHA
     ISKEPSPSTI INEESLNCAF LYPGLGLEFT GYLNYIGASQ KLRRDIFKEA IGDGKLYVEG
     RLPTTTAAPY LKEISCSRAI LVYQLFPSND SESKTTFADV VDSLENKGRI AGIKPKTRYE
     KDFYIVPSKG GEIPEILKDI LGSHNDERSE RFSRMKSDER TLFAFVVVKQ EFIH
//