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 27-MAR-2024, entry version 125.
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.ENSDARP00000045941; -.
DR PaxDb; 7955-ENSDARP00000111663; -.
DR GeneID; 503778; -.
DR KEGG; dre:503778; -.
DR AGR; ZFIN:ZDB-GENE-050302-10; -.
DR CTD; 5253; -.
DR ZFIN; ZDB-GENE-050302-10; phf2.
DR eggNOG; KOG1633; Eukaryota.
DR InParanoid; Q6P949; -.
DR OrthoDB; 2784357at2759; -.
DR Reactome; R-DRE-3214842; HDMs demethylate histones.
DR PRO; PR:Q6P949; -.
DR Proteomes; UP000000437; Chromosome 11.
DR Bgee; ENSDARG00000018691; Expressed in camera-type eye and 24 other cell types or 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 H3K9 demethylase activity; ISS:UniProtKB.
DR GO; GO:0035575; F:histone H4K20 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:0061188; P:negative regulation of rDNA heterochromatin formation; 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 GO; GO:0045815; P:transcription initiation-coupled chromatin remodeling; ISS:UniProtKB.
DR CDD; cd15641; PHD_PHF2; 1.
DR Gene3D; 1.20.58.1360; -; 1.
DR Gene3D; 2.60.120.650; Cupin; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 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 PANTHER; PTHR23123:SF14; LYSINE-SPECIFIC DEMETHYLASE PHF2; 1.
DR PANTHER; PTHR23123; PHD/F-BOX CONTAINING PROTEIN; 1.
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; SSF51197; Clavaminate synthase-like; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 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
//
