RPH1_YEAST
ID RPH1_YEAST Reviewed; 796 AA.
AC P39956; D3DM77;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 186.
DE RecName: Full=DNA damage-responsive transcriptional repressor RPH1;
GN Name=RPH1; OrderedLocusNames=YER169W;
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=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
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 DOMAIN ATYPICAL ZINC-FINGER.
RX PubMed=9171100; DOI=10.1093/nar/25.12.2464;
RA Boehm S., Frishman D., Mewes H.-W.;
RT "Variations of the C2H2 zinc finger motif in the yeast genome and
RT classification of yeast zinc finger proteins.";
RL Nucleic Acids Res. 25:2464-2469(1997).
RN [4]
RP FUNCTION IN TRANSCRIPTIONAL REPRESSION.
RX PubMed=10523651; DOI=10.1128/mcb.19.11.7630;
RA Jang Y.K., Wang L., Sancar G.B.;
RT "RPH1 and GIS1 are damage-responsive repressors of PHR1.";
RL Mol. Cell. Biol. 19:7630-7638(1999).
RN [5]
RP FUNCTION, AND PHOSPHORYLATION BY RAD53.
RX PubMed=11809875; DOI=10.1093/nar/30.3.643;
RA Kim E.M., Jang Y.K., Park S.D.;
RT "Phosphorylation of Rph1, a damage-responsive repressor of PHR1 in
RT Saccharomyces cerevisiae, is dependent upon Rad53 kinase.";
RL Nucleic Acids Res. 30:643-648(2002).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
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 [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-561 AND SER-689, 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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-652, AND IDENTIFICATION BY
RP 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-561 AND SER-575, 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 [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-399; SER-430; SER-459;
RP SER-557; SER-561; SER-575; SER-584 AND SER-689, AND IDENTIFICATION BY MASS
RP 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: Transcriptional repressor of photolyase PHR1. Recognizes and
CC binds the sequence AG(4) in the upstream repressing sequence of PHR1.
CC Derepresses PHR1 transcription when phosphorylated.
CC {ECO:0000269|PubMed:10523651, ECO:0000269|PubMed:11809875}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00537,
CC ECO:0000269|PubMed:14562095}.
CC -!- PTM: RAD53-dependent phosphorylated in response to DNA damage.
CC {ECO:0000269|PubMed:11809875}.
CC -!- MISCELLANEOUS: Present with 2229 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U18922; AAB64696.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07831.1; -; Genomic_DNA.
DR PIR; S50672; S50672.
DR RefSeq; NP_011096.1; NM_001179059.1.
DR PDB; 3OPT; X-ray; 2.20 A; A=1-373.
DR PDB; 3OPW; X-ray; 2.50 A; A=1-373.
DR PDBsum; 3OPT; -.
DR PDBsum; 3OPW; -.
DR AlphaFoldDB; P39956; -.
DR SMR; P39956; -.
DR BioGRID; 36922; 146.
DR DIP; DIP-5418N; -.
DR IntAct; P39956; 2.
DR STRING; 4932.YER169W; -.
DR iPTMnet; P39956; -.
DR MaxQB; P39956; -.
DR PaxDb; P39956; -.
DR PRIDE; P39956; -.
DR EnsemblFungi; YER169W_mRNA; YER169W; YER169W.
DR GeneID; 856916; -.
DR KEGG; sce:YER169W; -.
DR SGD; S000000971; RPH1.
DR VEuPathDB; FungiDB:YER169W; -.
DR eggNOG; KOG0958; Eukaryota.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_008557_0_0_1; -.
DR InParanoid; P39956; -.
DR OMA; NRVTLNI; -.
DR BioCyc; YEAST:G3O-30330-MON; -.
DR BRENDA; 1.14.11.69; 984.
DR Reactome; R-SCE-3214842; HDMs demethylate histones.
DR Reactome; R-SCE-5625886; Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
DR Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-SCE-9018519; Estrogen-dependent gene expression.
DR EvolutionaryTrace; P39956; -.
DR PRO; PR:P39956; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P39956; protein.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0001227; F:DNA-binding transcription repressor activity, RNA polymerase II-specific; IDA:SGD.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; IDA:SGD.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:SGD.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0010507; P:negative regulation of autophagy; IMP:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:SGD.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IGI:SGD.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF00096; zf-C2H2; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00355; ZnF_C2H2; 2.
DR SUPFAM; SSF57667; SSF57667; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Repressor; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..796
FT /note="DNA damage-responsive transcriptional repressor
FT RPH1"
FT /id="PRO_0000046849"
FT DOMAIN 14..55
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 193..355
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 709..732
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 738..763
FT /note="C2H2-type 2; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 599..692
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 774..796
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 455..471
FT /note="Bipartite nuclear localization signal"
FT COMPBIAS 599..627
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 631..653
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 654..673
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 399
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 430
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 459
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 557
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 561
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 575
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 584
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 652
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358"
FT MOD_RES 689
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT STRAND 9..17
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 27..32
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 35..38
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 41..46
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 50..53
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 62..67
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 74..91
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 98..104
FT /evidence="ECO:0007829|PDB:3OPT"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:3OPW"
FT HELIX 142..148
FT /evidence="ECO:0007829|PDB:3OPT"
FT TURN 149..151
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:3OPW"
FT HELIX 162..174
FT /evidence="ECO:0007829|PDB:3OPT"
FT TURN 175..178
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 182..188
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:3OPW"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 231..235
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 242..251
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 260..262
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 263..272
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 275..278
FT /evidence="ECO:0007829|PDB:3OPT"
FT TURN 285..287
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:3OPT"
FT HELIX 294..298
FT /evidence="ECO:0007829|PDB:3OPT"
FT TURN 299..301
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 314..317
FT /evidence="ECO:0007829|PDB:3OPT"
FT STRAND 323..338
FT /evidence="ECO:0007829|PDB:3OPT"
SQ SEQUENCE 796 AA; 90211 MW; 606C27836E1600F5 CRC64;
MTKLIAPSEI VGGVPVFKPT YEQFEDFYAY CKAINKYGMK SGVVKVIPPK EWKDKLDLPY
SAETLQKIKI KSPIQQHISG NKGLFMVQNV EKNKTYNIIQ WKDLSKDYVP PEDPKARRNS
RKGSVSKSTK LKLKNFESSF NIDDFEQFRT EYTIDLSDFQ NTERLKFLEE YYWKTLNFTT
PMYGADTPGS IFPEGLNVWN VAKLPNILDH METKVPGVND SYLYAGLWKA SFSWHLEDQD
LYSINYIHFG APKQWYSIPQ EDRFKFYKFM QEQFPEEAKN CPEFLRHKMF LASPKLLQEN
GIRCNEIVHH EGEFMITYPY GYHAGFNYGY NLAESVNFAL EEWLPIGKKA GKCHCISDSV
EIDVKKLAKS WRDNNKESKG TPPLNQLPNP AMPLLHRPTL KEMESSSLRS TSPDVGHFSN
FKSKSSGVSS PLLSRMKDYS NIVEPTLEDP TLKLKRISSF QEQPLNKLLK RETSQTAMLT
DHEDNIVAMS LTSMANSAAS SPRLPLSRLN SSNELSNAQP LLDMTNNTLA FPRPNGPSGL
NPLLYISNKN ISGISHSAPH SPVNPNISLI KRVKSPNIVT LNISRESSRS PIALNYEARQ
QHSQQHSFST PSTVSNLSTS VLGPLSDTND IKTPHPERPN HKTANRILKK ESPVETSKSN
LILSKVASTR QEDSFTSRND DLDKEQGSSP LNSKFAPEEI VLSGKNKIYI CKECQRKFSS
GHHLTRHKKS VHSGEKPHSC PKCGKRFKRR DHVLQHLNKK IPCISNETTV DAPIMNPTVQ
PQDGKAAINQ QSTPLN
