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PHF2_DANRE
ID   PHF2_DANRE              Reviewed;        1063 AA.
AC   Q6P949; E7EZ72;
DT   05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 3.
DT   03-AUG-2022, entry version 117.
DE   RecName: Full=Lysine-specific demethylase phf2;
DE            EC=1.14.11.-;
DE   AltName: Full=PHD finger protein 2;
GN   Name=phf2;
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
RX   PubMed=23594743; DOI=10.1038/nature12111;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA   Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA   Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA   Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA   Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA   Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA   Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA   McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA   Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA   Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA   Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA   Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA   Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA   Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA   Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA   Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA   Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA   Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA   Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA   Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA   de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA   Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-899 (ISOFORM 1).
RC   TISSUE=Eye;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (NOV-2003) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Lysine demethylase that demethylates both histones and non-
CC       histone proteins. Mediates demethylation of dimethylated 'Lys-9' of
CC       histone H3 (H3K9me2). Recruited to trimethylated 'Lys-4' of histone H3
CC       (H3K4me3) at rDNA promoters and promotes expression of rDNA (By
CC       similarity). {ECO:0000250|UniProtKB:O75151}.
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:O75151}. Chromosome, centromere, kinetochore
CC       {ECO:0000250|UniProtKB:O75151}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q6P949-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q6P949-2; Sequence=VSP_041562;
CC   -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D
CC       subfamily. {ECO:0000305}.
CC   -!- CAUTION: In contrast to the related histone demethylases jhdm1d and
CC       phf8, the conserved active His in position 321 is replaced by an Asn.
CC       However, the presence of an Asn residue neither affects binding to the
CC       catalytic iron nor abolishes demethylase activity. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAH60927.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
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DR   EMBL; BX601648; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC060927; AAH60927.1; ALT_SEQ; mRNA.
DR   RefSeq; NP_001189347.1; NM_001202418.1. [Q6P949-2]
DR   AlphaFoldDB; Q6P949; -.
DR   SMR; Q6P949; -.
DR   STRING; 7955.ENSDARP00000111663; -.
DR   PRIDE; Q6P949; -.
DR   Ensembl; ENSDART00000125352; ENSDARP00000111663; ENSDARG00000018691. [Q6P949-2]
DR   GeneID; 503778; -.
DR   KEGG; dre:503778; -.
DR   CTD; 5253; -.
DR   ZFIN; ZDB-GENE-050302-10; phf2.
DR   eggNOG; KOG1633; Eukaryota.
DR   GeneTree; ENSGT00940000158148; -.
DR   InParanoid; Q6P949; -.
DR   Reactome; R-DRE-3214842; HDMs demethylate histones.
DR   PRO; PR:Q6P949; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 11.
DR   Bgee; ENSDARG00000018691; Expressed in camera-type eye and 24 other tissues.
DR   ExpressionAtlas; Q6P949; baseline and differential.
DR   GO; GO:0000776; C:kinetochore; ISS:UniProtKB.
DR   GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR   GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR   GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; ISS:UniProtKB.
DR   GO; GO:0035575; F:histone H4-methyl-lysine-20 demethylase activity; ISS:UniProtKB.
DR   GO; GO:0005506; F:iron ion binding; ISS:UniProtKB.
DR   GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB.
DR   GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
DR   GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0045815; P:epigenetic maintenance of chromatin in transcription-competent conformation; ISS:UniProtKB.
DR   GO; GO:0035574; P:histone H4-K20 demethylation; ISS:UniProtKB.
DR   GO; GO:0061188; P:negative regulation of ribosomal DNA heterochromatin assembly; ISS:UniProtKB.
DR   GO; GO:0006482; P:protein demethylation; ISS:UniProtKB.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   Gene3D; 3.30.40.10; -; 1.
DR   InterPro; IPR041070; JHD.
DR   InterPro; IPR003347; JmjC_dom.
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; PF17811; JHD; 1.
DR   Pfam; PF02373; JmjC; 1.
DR   Pfam; PF00628; PHD; 1.
DR   SMART; SM00558; JmjC; 1.
DR   SMART; SM00249; PHD; 1.
DR   SUPFAM; SSF57903; SSF57903; 1.
DR   PROSITE; PS51184; JMJC; 1.
DR   PROSITE; PS01359; ZF_PHD_1; 1.
DR   PROSITE; PS50016; ZF_PHD_2; 1.
PE   2: Evidence at transcript level;
KW   Activator; Alternative splicing; Centromere; Chromatin regulator;
KW   Chromosome; Dioxygenase; Iron; Kinetochore; Metal-binding; Nucleus;
KW   Oxidoreductase; Phosphoprotein; Reference proteome; Transcription;
KW   Transcription regulation; Zinc; Zinc-finger.
FT   CHAIN           1..1063
FT                   /note="Lysine-specific demethylase phf2"
FT                   /id="PRO_0000399818"
FT   DOMAIN          197..353
FT                   /note="JmjC"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   ZN_FING         5..56
FT                   /note="PHD-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          448..546
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          704..761
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          773..864
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          879..1045
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        448..462
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        509..536
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        719..749
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        773..828
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        889..906
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        962..978
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        979..1004
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1017..1033
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         246
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         249
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         251
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         259
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         266
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250"
FT   BINDING         321
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   MOD_RES         1021
FT                   /note="Phosphoserine; by PKA"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         444..452
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_041562"
FT   CONFLICT        832
FT                   /note="G -> R (in Ref. 2; AAH60927)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1063 AA;  118582 MW;  35A04F87871BBD85 CRC64;
     MATVPVYCIC RLPYDVTQFM IECDACKDWF HGSCVGVDED EAPDIDIYHC PNCEKTHGKS
     TLKKKKSWNK HDTGQSGDVR PVQNGSQVFI KELRSRTFPS SEDVVVKLSG SQLTLEYLEE
     NGFNEPILIQ KKDGLGMAMP APTFYVSDVE NYVGPDVLVD VVDVTKQTDS KMKLKEFVDY
     YYSTNRKKVL NVINLEFSDA RMANIVESPQ IVRKLSWVEN YWPDDALLGK PKVSKYCLIC
     VKDSYTDFHI ECGGASVWYH VLKGEKIFFL IKPTSANLSL YERWRSSSNH SEMFFADQVD
     KCYKCTLKQG QTLFIPSGWI NAILTPVDCL AFSGHFVHSL SVEMQMRAYE VEKRLKVASL
     TPFSNFETAC WYVGKYYLEQ FKGLHKANKQ PPPYLVHGAK IVNGAFRSWT KKQALLEHED
     ELPENMKPAQ LIKDLAKEIR IAEVKQVVSD SQNATKAIKS EPSNSKPPAE EPPSALSEPE
     EPMSPAHVSS PSGDKPARKK VPKPPKMPKA PKPPKEPKIK EGGKKKAKKV KEGVIPEKKP
     SSLAALESHA KDILNKMDQP KKLIKTGMSI MEKETNKPND VKKFEMIREH NKNKTESKWK
     YKNSKPDSLL KMEEEHKFDK SLLSHKDNKF AFSLSNKKLL GSKMLKTQTN SSVFGSIQNI
     KEEKPKPVRD EYEYVSDEGE LKIEEFPIRR KKNAVKREFS FLSNIKEPIQ PSKKPKLPPS
     DMKSPDTSDE ESLHIDTEAK TDVKGRNSKV SKKKGGSSAG ILDLLQASKQ VGGIDYSNNS
     QPPASPSTQE AIQGMLSMAN LQSSDSCLQP FWSNSQAKNN SHSSAASKKP SGAAGAGGNS
     KRPAKRLPKK TQKSSSVDSS DMFDDDQDHL EACFKDSDYV YPSLESEEDN PIFKSRSKKR
     KNTDDTPYSP TARVGPTVPR QERPAREGAR VASIETGLAA AAAKLSHQEE QKIKKKKKSA
     KKKPIVAEES HKLSHDSSSP EPTPDSESNM ADHEYSTGTG KSAGGSQPMA PGVFLSHRRP
     SSSSSSQNAS SVLPAKRLKK GMATAKQRLG KILKIHRNGK LLL
 
 
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