ID KDM7A_DANRE Reviewed; 875 AA.
AC Q5RHD1; A5PL83;
DT 18-MAY-2010, integrated into UniProtKB/Swiss-Prot.
DT 18-MAY-2010, sequence version 2.
DT 27-MAR-2024, entry version 122.
DE RecName: Full=Lysine-specific demethylase 7A;
DE Short=DrKDM7a;
DE EC=1.14.11.-;
DE AltName: Full=JmjC domain-containing histone demethylation protein 1D-A;
GN Name=kdm7a; Synonyms=jhdm1da, kdm7; ORFNames=si:dkey-105o6.2;
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 1-611.
RC TISSUE=Intestine;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=20194436; DOI=10.1101/gad.1864410;
RA Tsukada Y., Ishitani T., Nakayama K.I.;
RT "KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions
RT in brain development.";
RL Genes Dev. 24:432-437(2010).
CC -!- FUNCTION: Histone demethylase required for brain development.
CC Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2
CC and H3K27me2, respectively) of histone H3 and monomethylated histone H4
CC 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone
CC code (By similarity). {ECO:0000250, ECO:0000269|PubMed:20194436}.
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Predominantly expressed in brain.
CC {ECO:0000269|PubMed:20194436}.
CC -!- DOMAIN: The PHD-type zinc finger mediates the binding to H3K4me3.
CC Binding to H3K4me3 prevents its access to H3K9me2 (By similarity).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family. JHDM1D
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI42783.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
CC Sequence=CAI12074.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; BX537168; CAI12074.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC142782; AAI42783.1; ALT_SEQ; mRNA.
DR AlphaFoldDB; Q5RHD1; -.
DR SMR; Q5RHD1; -.
DR STRING; 7955.ENSDARP00000111845; -.
DR PaxDb; 7955-ENSDARP00000104491; -.
DR AGR; ZFIN:ZDB-GENE-030131-9829; -.
DR ZFIN; ZDB-GENE-030131-9829; kdm7aa.
DR eggNOG; KOG1633; Eukaryota.
DR InParanoid; Q5RHD1; -.
DR OMA; IRDERCH; -.
DR PhylomeDB; Q5RHD1; -.
DR TreeFam; TF106480; -.
DR PRO; PR:Q5RHD1; -.
DR Proteomes; UP000000437; Genome assembly.
DR Bgee; ENSDARG00000018111; Expressed in testis and 37 other cell types or tissues.
DR ExpressionAtlas; Q5RHD1; baseline.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; ISS:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0071558; F:histone H3K27me2/H3K27me3 demethylase activity; IDA:ZFIN.
DR GO; GO:0051864; F:histone H3K36 demethylase activity; ISS:UniProtKB.
DR GO; GO:0032454; F:histone H3K9 demethylase activity; IDA:ZFIN.
DR GO; GO:0035575; F:histone H4K20 demethylase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0030901; P:midbrain development; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd15640; PHD_KDM7; 1.
DR Gene3D; 1.20.58.1360; -; 1.
DR Gene3D; 2.60.120.650; Cupin; 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 PANTHER; PTHR23123:SF15; LYSINE-SPECIFIC DEMETHYLASE 7A; 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 Chromatin regulator; Dioxygenase; Iron; Metal-binding; Neurogenesis;
KW Nucleus; Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..875
FT /note="Lysine-specific demethylase 7A"
FT /id="PRO_0000394249"
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 442..506
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 629..710
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 742..820
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 450..469
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 477..505
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 629..652
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 653..673
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 742..759
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 797..811
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 246
FT /ligand="substrate"
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 266
FT /ligand="substrate"
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 CONFLICT 182
FT /note="Y -> H (in Ref. 2; AAI42783)"
FT /evidence="ECO:0000305"
FT CONFLICT 454
FT /note="S -> R (in Ref. 2; AAI42783)"
FT /evidence="ECO:0000305"
FT CONFLICT 471
FT /note="Q -> K (in Ref. 2; AAI42783)"
FT /evidence="ECO:0000305"
FT CONFLICT 588
FT /note="V -> L (in Ref. 2; AAI42783)"
FT /evidence="ECO:0000305"
FT CONFLICT 596
FT /note="I -> M (in Ref. 2; AAI42783)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 875 AA; 98827 MW; B257F3649D95AFF4 CRC64;
MAAAPLYCVC RQPYDVNRFM IECDICKDWF HGSCVQVVEH HAADIDVYHC PNCEPIHGPY
MMKKHNNWHR HDYTEPNDGT RPVQAGTAVF VKELQARSFA SGDILVQMQG NQVTKRFLEK
EGFNYPIVVH DLDGLGLKLP PPSFSVSDVE HYVGANKVID VIDVAKQADS KMKLGEFVKY
YYQPERPKVL NVISLEFSDT RMSNLVVVPD IAQKMSWVEN YWPDDSFFPK PFVQKYCLMG
MKNSYTDFHI DFGGTSVWYH VLWGEKIFYL IKPTKANLAL YEAWSSSPNQ SEVFFGEKVD
KCYKCVVKQG TTILLPTGWI HAVLTSQDSM AFGGNFLHNL NIDMQLRCYE MERRLKTPDL
FKFPYFEAIC WYVAKNLLET LKELRENKCE AQGFLVNGVK ALISSLKMWL RRELTQPNSE
VPDNIRPGHL IKALSKEIRH LEDDSNKAVK TQGSAECSLS RSTLEKGDQA QQAARRLQDH
HHHRRRHHHH HHHHHHHHHH HHSRKLPSNL DVLELHTLEV LKRLEVGQLK EDSAFSSKVN
GKFKKVCPVP AAAVEASHDN ALRLVMCNGK IIRERMPITN VAATVNAVEM YHKHRIKLER
IPMCPEEKVK KEKCEDEFGV QCTIKKPVSQ GESVQTELRT ESPHLASSDS DSKAGDSAEK
CSLESESSDG EDGGSQRDSG TFVEHLNSHR HSHHKQALKR ERPTSPNTDC AIQGMLSMAG
LLCPQASGGA ADILQQRWWA SQGNGSSTSS SSDMWDSSEP CSAPRSPDAE DGSLGEEYSY
RESSLSPPLH PSKRHAPNPT PVSNQATKGK RPKKGQATAK QRLGKILKMS RHKGLFLMKP
MVFLIPQQGG TPLDPQFLLQ SSSICVFPPP LIVSG
//
