BYE1_YEAST
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 03-AUG-2022, entry version 162.
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; 109.
DR MINT; P36106; -.
DR STRING; 4932.YKL005C; -.
DR iPTMnet; P36106; -.
DR MaxQB; P36106; -.
DR PaxDb; P36106; -.
DR PRIDE; P36106; -.
DR EnsemblFungi; YKL005C_mRNA; YKL005C; YKL005C.
DR GeneID; 853865; -.
DR KEGG; sce:YKL005C; -.
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 BioCyc; YEAST:G3O-31815-MON; -.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
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 Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.
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:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0006351; P:transcription, DNA-templated; IBA:GO_Central.
DR DisProt; DP02476; -.
DR Gene3D; 1.10.472.30; -; 1.
DR Gene3D; 3.30.40.10; -; 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 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; SSF46942; 1.
DR SUPFAM; SSF57903; SSF57903; 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
