ID   KDM5D_HUMAN             Reviewed;        1539 AA.
AC   Q9BY66; A2RU19; A6H8V7; B7ZLX1; Q92509; Q92809; Q9HCU1;
DT   24-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT   24-OCT-2001, sequence version 2.
DT   12-OCT-2022, entry version 189.
DE   RecName: Full=Lysine-specific demethylase 5D;
DE            EC=1.14.11.67 {ECO:0000269|PubMed:17320160};
DE   AltName: Full=Histocompatibility Y antigen;
DE            Short=H-Y;
DE   AltName: Full=Histone demethylase JARID1D;
DE   AltName: Full=Jumonji/ARID domain-containing protein 1D;
DE   AltName: Full=Protein SmcY;
DE   AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase 5D {ECO:0000305};
GN   Name=KDM5D; Synonyms=HY, HYA, JARID1D, KIAA0234, SMCY;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND VARIANT LEU-1186.
RX   PubMed=8841177; DOI=10.1038/ng1096-128;
RA   Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S.,
RA   Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A.,
RA   Vandeberg J.;
RT   "Gene sequence and evolutionary conservation of human SMCY.";
RL   Nat. Genet. 14:128-129(1996).
RN   [2]
RP   ERRATUM OF PUBMED:8841177.
RA   Kent-First M.G., Maffitt M., Muallem A., Brisco P., Shultz J., Ekenberg S.,
RA   Agulnik A.I., Agulnik S.I., Shramm D., Bavister B., Abdul-Mawgood A.,
RA   Vandeberg J.;
RL   Nat. Genet. 14:252-252(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   TISSUE=Bone marrow;
RX   PubMed=9039502; DOI=10.1093/dnares/3.5.321;
RA   Nagase T., Seki N., Ishikawa K., Ohira M., Kawarabayasi Y., Ohara O.,
RA   Tanaka A., Kotani H., Miyajima N., Nomura N.;
RT   "Prediction of the coding sequences of unidentified human genes. VI. The
RT   coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of
RT   cDNA clones from cell line KG-1 and brain.";
RL   DNA Res. 3:321-329(1996).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
RX   PubMed=10861003; DOI=10.1073/pnas.97.13.7354;
RA   Shen P., Wang F., Underhill P.A., Franco C., Yang W.-H., Roxas A., Sung R.,
RA   Lin A.A., Hyman R.W., Vollrath D., Davis R.W., Cavalli-Sforza L.L.,
RA   Oefner P.J.;
RT   "Population genetic implications from sequence variation in four Y
RT   chromosome genes.";
RL   Proc. Natl. Acad. Sci. U.S.A. 97:7354-7359(2000).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=12815422; DOI=10.1038/nature01722;
RA   Skaletsky H., Kuroda-Kawaguchi T., Minx P.J., Cordum H.S., Hillier L.W.,
RA   Brown L.G., Repping S., Pyntikova T., Ali J., Bieri T., Chinwalla A.,
RA   Delehaunty A., Delehaunty K., Du H., Fewell G., Fulton L., Fulton R.,
RA   Graves T.A., Hou S.-F., Latrielle P., Leonard S., Mardis E., Maupin R.,
RA   McPherson J., Miner T., Nash W., Nguyen C., Ozersky P., Pepin K., Rock S.,
RA   Rohlfing T., Scott K., Schultz B., Strong C., Tin-Wollam A., Yang S.-P.,
RA   Waterston R.H., Wilson R.K., Rozen S., Page D.C.;
RT   "The male-specific region of the human Y chromosome is a mosaic of discrete
RT   sequence classes.";
RL   Nature 423:825-837(2003).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA   Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA   Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA   Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA   Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA   Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA   Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA   Hunkapiller M.W., Myers E.W., Venter J.C.;
RL   Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [8]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 1-457 (ISOFORM 1).
RX   PubMed=9060413; DOI=10.1007/s003359900372;
RA   Agulnik A.I., Bishop C.E., Lerner J.L., Agulnik S.I., Solovyev V.V.;
RT   "Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian
RT   evolution is male driven.";
RL   Mamm. Genome 8:134-138(1997).
RN   [9]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1340-1478.
RC   TISSUE=Blood;
RA   Poloumienko A., Blecher S.;
RT   "Exon-intron structure of SMCX and SMCY genes in bovine and swine.";
RL   Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases.
RN   [10]
RP   FUNCTION, COFACTOR, INTERACTION WITH PCGF6, AND MUTAGENESIS OF HIS-534 AND
RP   GLU-536.
RX   PubMed=17320162; DOI=10.1016/j.cell.2007.02.004;
RA   Lee M.G., Norman J., Shilatifard A., Shiekhattar R.;
RT   "Physical and functional association of a trimethyl H3K4 demethylase and
RT   Ring6a/MBLR, a polycomb-like protein.";
RL   Cell 128:877-887(2007).
RN   [11]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=17320160; DOI=10.1016/j.cell.2007.02.017;
RA   Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H.,
RA   Whetstine J.R., Bonni A., Roberts T.M., Shi Y.;
RT   "The X-linked mental retardation gene SMCX/JARID1C defines a family of
RT   histone H3 lysine 4 demethylases.";
RL   Cell 128:1077-1088(2007).
RN   [12]
RP   FUNCTION.
RX   PubMed=17351630; DOI=10.1038/nsmb1217;
RA   Eissenberg J.C., Lee M.G., Schneider J., Ilvarsonn A., Shiekhattar R.,
RA   Shilatifard A.;
RT   "The trithorax-group gene in Drosophila little imaginal discs encodes a
RT   trimethylated histone H3 Lys4 demethylase.";
RL   Nat. Struct. Mol. Biol. 14:344-346(2007).
RN   [13]
RP   INTERACTION WITH MSH5.
RX   PubMed=18459961; DOI=10.1111/j.1365-2443.2008.01193.x;
RA   Akimoto C., Kitagawa H., Matsumoto T., Kato S.;
RT   "Spermatogenesis-specific association of SMCY and MSH5.";
RL   Genes Cells 13:623-633(2008).
RN   [14]
RP   FUNCTION, AND TISSUE SPECIFICITY.
RX   PubMed=26747897; DOI=10.1158/0008-5472.can-15-0906;
RA   Li N., Dhar S.S., Chen T.Y., Kan P.Y., Wei Y., Kim J.H., Chan C.H.,
RA   Lin H.K., Hung M.C., Lee M.G.;
RT   "JARID1D is a suppressor and prognostic marker of prostate cancer invasion
RT   and metastasis.";
RL   Cancer Res. 76:831-843(2016).
RN   [15]
RP   BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, AND COFACTOR.
RX   PubMed=27427228; DOI=10.1016/j.chembiol.2016.06.006;
RA   Horton J.R., Liu X., Gale M., Wu L., Shanks J.R., Zhang X., Webber P.J.,
RA   Bell J.S., Kales S.C., Mott B.T., Rai G., Jansen D.J., Henderson M.J.,
RA   Urban D.J., Hall M.D., Simeonov A., Maloney D.J., Johns M.A., Fu H.,
RA   Jadhav A., Vertino P.M., Yan Q., Cheng X.;
RT   "Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by
RT   Diverse Compounds.";
RL   Cell Chem. Biol. 23:769-781(2016).
RN   [16]
RP   FUNCTION, INTERACTION WITH ZMYND8, AND SUBCELLULAR LOCATION.
RX   PubMed=27477906; DOI=10.1016/j.molcel.2016.06.035;
RA   Li N., Li Y., Lv J., Zheng X., Wen H., Shen H., Zhu G., Chen T.Y.,
RA   Dhar S.S., Kan P.Y., Wang Z., Shiekhattar R., Shi X., Lan F., Chen K.,
RA   Li W., Li H., Lee M.G.;
RT   "ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the
RT   expression of metastasis-linked genes.";
RL   Mol. Cell 63:470-484(2016).
RN   [17]
RP   FUNCTION, INTERACTION WITH AR, SUBCELLULAR LOCATION, AND INVOLVEMENT IN
RP   DOCETAXEL SENSITIVITY.
RX   PubMed=27185910; DOI=10.1073/pnas.1600420113;
RA   Komura K., Jeong S.H., Hinohara K., Qu F., Wang X., Hiraki M., Azuma H.,
RA   Lee G.S., Kantoff P.W., Sweeney C.J.;
RT   "Resistance to docetaxel in prostate cancer is associated with androgen
RT   receptor activation and loss of KDM5D expression.";
RL   Proc. Natl. Acad. Sci. U.S.A. 113:6259-6264(2016).
RN   [18]
RP   STRUCTURE BY NMR OF 79-384.
RG   RIKEN structural genomics initiative (RSGI);
RT   "Solution structure of the PHD domain and of the ARID domain of
RT   JARID1D/SMCY protein.";
RL   Submitted (APR-2008) to the PDB data bank.
CC   -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-4' of
CC       histone H3, thereby playing a central role in histone code. Does not
CC       demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79'
CC       or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not
CC       monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved
CC       in transcriptional repression of diverse metastasis-associated genes;
CC       in this function seems to cooperate with ZMYND8. Suppresses prostate
CC       cancer cell invasion. Regulates androgen receptor (AR) transcriptional
CC       activity by demethylating H3K4me3 active transcription marks.
CC       {ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320162,
CC       ECO:0000269|PubMed:17351630, ECO:0000269|PubMed:26747897,
CC       ECO:0000269|PubMed:27185910, ECO:0000269|PubMed:27427228,
CC       ECO:0000269|PubMed:27477906}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-
CC         [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone
CC         H3] + 3 succinate; Xref=Rhea:RHEA:60208, Rhea:RHEA-COMP:15537,
CC         Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969,
CC         ChEBI:CHEBI:30031, ChEBI:CHEBI:61961; EC=1.14.11.67;
CC         Evidence={ECO:0000269|PubMed:17320160};
CC   -!- COFACTOR:
CC       Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
CC         Evidence={ECO:0000269|PubMed:17320162};
CC   -!- COFACTOR:
CC       Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC         Evidence={ECO:0000269|PubMed:17320162};
CC       Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:17320162};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=10 uM for 2-oxoglutarate {ECO:0000269|PubMed:27427228};
CC         KM=6.2 uM for histone H3K4me3 {ECO:0000269|PubMed:27427228};
CC         Note=kcat is 2.6 min(-1) and 3.0 min(-1) for 2-oxoglutarate and
CC         histone H3K4me3, respectively. {ECO:0000269|PubMed:27427228};
CC   -!- SUBUNIT: Interacts with PCGF6, MSH5, ZMYND8, AR.
CC       {ECO:0000269|PubMed:17320162, ECO:0000269|PubMed:18459961,
CC       ECO:0000269|PubMed:27185910, ECO:0000269|PubMed:27477906}.
CC   -!- INTERACTION:
CC       Q9BY66; P10275: AR; NbExp=2; IntAct=EBI-1246860, EBI-608057;
CC       Q9BY66-3; P10275: AR; NbExp=2; IntAct=EBI-12559887, EBI-608057;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:27185910,
CC       ECO:0000269|PubMed:27477906, ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC         Comment=Additional isoforms seem to exist.;
CC       Name=1;
CC         IsoId=Q9BY66-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9BY66-2; Sequence=VSP_000317;
CC       Name=3;
CC         IsoId=Q9BY66-3; Sequence=VSP_043320;
CC   -!- TISSUE SPECIFICITY: Expression is highly down-regulated in metastatic
CC       prostate tumors. {ECO:0000269|PubMed:26747897}.
CC   -!- DOMAIN: The JmjC domain is required for enzymatic activity.
CC   -!- MISCELLANEOUS: Involved in sensitivity to docetaxel.
CC       {ECO:0000269|PubMed:27185910}.
CC   -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAA13241.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; U52191; AAC50806.1; -; mRNA.
DR   EMBL; D87072; BAA13241.2; ALT_INIT; mRNA.
DR   EMBL; AF273841; AAG00951.1; -; Genomic_DNA.
DR   EMBL; AC010889; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CH471202; EAW54663.1; -; Genomic_DNA.
DR   EMBL; BC132721; AAI32722.1; -; mRNA.
DR   EMBL; BC144102; AAI44103.1; -; mRNA.
DR   EMBL; BC146767; AAI46768.1; -; mRNA.
DR   EMBL; U52365; AAC51135.1; -; mRNA.
DR   EMBL; AF134849; AAK27839.1; -; Genomic_DNA.
DR   CCDS; CCDS14794.1; -. [Q9BY66-1]
DR   CCDS; CCDS55554.1; -. [Q9BY66-2]
DR   CCDS; CCDS55555.1; -. [Q9BY66-3]
DR   RefSeq; NP_001140177.1; NM_001146705.1. [Q9BY66-3]
DR   RefSeq; NP_001140178.1; NM_001146706.1. [Q9BY66-2]
DR   RefSeq; NP_004644.2; NM_004653.4. [Q9BY66-1]
DR   PDB; 2E6R; NMR; -; A=306-384.
DR   PDB; 2YQE; NMR; -; A=79-171.
DR   PDBsum; 2E6R; -.
DR   PDBsum; 2YQE; -.
DR   AlphaFoldDB; Q9BY66; -.
DR   BMRB; Q9BY66; -.
DR   SMR; Q9BY66; -.
DR   BioGRID; 113891; 4.
DR   IntAct; Q9BY66; 4.
DR   BindingDB; Q9BY66; -.
DR   DrugBank; DB00126; Ascorbic acid.
DR   iPTMnet; Q9BY66; -.
DR   PhosphoSitePlus; Q9BY66; -.
DR   BioMuta; KDM5D; -.
DR   DMDM; 17368706; -.
DR   EPD; Q9BY66; -.
DR   jPOST; Q9BY66; -.
DR   MassIVE; Q9BY66; -.
DR   MaxQB; Q9BY66; -.
DR   PaxDb; Q9BY66; -.
DR   PeptideAtlas; Q9BY66; -.
DR   PRIDE; Q9BY66; -.
DR   ProteomicsDB; 79591; -. [Q9BY66-1]
DR   ProteomicsDB; 79592; -. [Q9BY66-2]
DR   ProteomicsDB; 79593; -. [Q9BY66-3]
DR   ABCD; Q9BY66; 1 sequenced antibody.
DR   Antibodypedia; 21879; 55 antibodies from 25 providers.
DR   DNASU; 8284; -.
DR   Ensembl; ENST00000317961.9; ENSP00000322408.4; ENSG00000012817.16. [Q9BY66-1]
DR   Ensembl; ENST00000382806.6; ENSP00000372256.2; ENSG00000012817.16. [Q9BY66-2]
DR   Ensembl; ENST00000541639.5; ENSP00000444293.1; ENSG00000012817.16. [Q9BY66-3]
DR   GeneID; 8284; -.
DR   KEGG; hsa:8284; -.
DR   MANE-Select; ENST00000317961.9; ENSP00000322408.4; NM_004653.5; NP_004644.2.
DR   UCSC; uc004fug.4; human. [Q9BY66-1]
DR   CTD; 8284; -.
DR   DisGeNET; 8284; -.
DR   GeneCards; KDM5D; -.
DR   GeneReviews; KDM5D; -.
DR   HGNC; HGNC:11115; KDM5D.
DR   HPA; ENSG00000012817; Low tissue specificity.
DR   MalaCards; KDM5D; -.
DR   MIM; 426000; gene.
DR   neXtProt; NX_Q9BY66; -.
DR   OpenTargets; ENSG00000012817; -.
DR   PharmGKB; PA35965; -.
DR   VEuPathDB; HostDB:ENSG00000012817; -.
DR   GeneTree; ENSGT00940000161236; -.
DR   HOGENOM; CLU_000991_2_2_1; -.
DR   InParanoid; Q9BY66; -.
DR   OMA; CIELPQI; -.
DR   OrthoDB; 664180at2759; -.
DR   PhylomeDB; Q9BY66; -.
DR   TreeFam; TF106476; -.
DR   BioCyc; MetaCyc:ENSG00000012817-MON; -.
DR   BRENDA; 1.14.11.67; 2681.
DR   PathwayCommons; Q9BY66; -.
DR   Reactome; R-HSA-3214842; HDMs demethylate histones.
DR   SignaLink; Q9BY66; -.
DR   SIGNOR; Q9BY66; -.
DR   BioGRID-ORCS; 8284; 12 hits in 740 CRISPR screens.
DR   ChiTaRS; KDM5D; human.
DR   EvolutionaryTrace; Q9BY66; -.
DR   GeneWiki; JARID1D; -.
DR   GenomeRNAi; 8284; -.
DR   Pharos; Q9BY66; Tbio.
DR   PRO; PR:Q9BY66; -.
DR   Proteomes; UP000005640; Chromosome Y.
DR   RNAct; Q9BY66; protein.
DR   Bgee; ENSG00000012817; Expressed in apex of heart and 188 other tissues.
DR   ExpressionAtlas; Q9BY66; baseline and differential.
DR   Genevisible; Q9BY66; HS.
DR   GO; GO:0001650; C:fibrillar center; IDA:HPA.
DR   GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR   GO; GO:0032453; F:histone H3-methyl-lysine-4 demethylase activity; IDA:MGI.
DR   GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0050681; F:nuclear androgen receptor binding; IDA:UniProtKB.
DR   GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR   GO; GO:0034720; P:histone H3-K4 demethylation; IDA:MGI.
DR   GO; GO:0060765; P:regulation of androgen receptor signaling pathway; IMP:UniProtKB.
DR   GO; GO:0002457; P:T cell antigen processing and presentation; IEA:Ensembl.
DR   Gene3D; 1.10.150.60; -; 1.
DR   Gene3D; 3.30.40.10; -; 2.
DR   InterPro; IPR001606; ARID_dom.
DR   InterPro; IPR036431; ARID_dom_sf.
DR   InterPro; IPR003347; JmjC_dom.
DR   InterPro; IPR003349; JmjN.
DR   InterPro; IPR013637; Lys_sp_deMease-like_dom.
DR   InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR   InterPro; IPR004198; Znf_C5HC2.
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; PF01388; ARID; 1.
DR   Pfam; PF02373; JmjC; 1.
DR   Pfam; PF02375; JmjN; 1.
DR   Pfam; PF00628; PHD; 1.
DR   Pfam; PF08429; PLU-1; 1.
DR   Pfam; PF02928; zf-C5HC2; 1.
DR   SMART; SM00501; BRIGHT; 1.
DR   SMART; SM00558; JmjC; 1.
DR   SMART; SM00545; JmjN; 1.
DR   SMART; SM00249; PHD; 2.
DR   SUPFAM; SSF46774; SSF46774; 1.
DR   SUPFAM; SSF57903; SSF57903; 2.
DR   PROSITE; PS51011; ARID; 1.
DR   PROSITE; PS51184; JMJC; 1.
DR   PROSITE; PS51183; JMJN; 1.
DR   PROSITE; PS01359; ZF_PHD_1; 2.
DR   PROSITE; PS50016; ZF_PHD_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative splicing; Chromatin regulator; Dioxygenase; Iron;
KW   Isopeptide bond; Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein;
KW   Reference proteome; Repeat; Transcription; Transcription regulation;
KW   Ubl conjugation; Zinc; Zinc-finger.
FT   CHAIN           1..1539
FT                   /note="Lysine-specific demethylase 5D"
FT                   /id="PRO_0000200588"
FT   DOMAIN          14..55
FT                   /note="JmjN"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT   DOMAIN          79..169
FT                   /note="ARID"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00355"
FT   DOMAIN          458..624
FT                   /note="JmjC"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   ZN_FING         316..362
FT                   /note="PHD-type 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   ZN_FING         697..749
FT                   /note="C5HC2"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   ZN_FING         1174..1235
FT                   /note="PHD-type 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT   REGION          192..228
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1429..1521
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        197..211
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        212..228
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1452..1471
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1478..1493
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1494..1521
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         430
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   BINDING         504
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   BINDING         506
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   BINDING         512
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   BINDING         514
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   BINDING         522
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:P29375"
FT   BINDING         592
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT   MOD_RES         291
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   MOD_RES         307
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   MOD_RES         884
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   MOD_RES         1346
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   CROSSLNK        205
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   CROSSLNK        229
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   CROSSLNK        244
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   CROSSLNK        272
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:P41229"
FT   VAR_SEQ         118..174
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:15489334,
FT                   ECO:0000303|PubMed:9039502"
FT                   /id="VSP_000317"
FT   VAR_SEQ         457
FT                   /note="K -> KRQSLTVLTRLISSFWAQAVLPPWPPKVLGLQ (in isoform
FT                   3)"
FT                   /evidence="ECO:0000303|PubMed:15489334"
FT                   /id="VSP_043320"
FT   VARIANT         1186
FT                   /note="V -> L (in dbSNP:rs1050807)"
FT                   /evidence="ECO:0000269|PubMed:8841177"
FT                   /id="VAR_032991"
FT   MUTAGEN         534
FT                   /note="H->A: Abolishes enzymatic activity; when associated
FT                   with A-536."
FT                   /evidence="ECO:0000269|PubMed:17320162"
FT   MUTAGEN         536
FT                   /note="E->A: Abolishes enzymatic activity; when associated
FT                   with A-534."
FT                   /evidence="ECO:0000269|PubMed:17320162"
FT   CONFLICT        327
FT                   /note="D -> N (in Ref. 1; AAC50806 and 8; AAC51135)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1285
FT                   /note="S -> F (in Ref. 1; AAC50806)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1352
FT                   /note="P -> L (in Ref. 9; AAK27839)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        1391
FT                   /note="D -> G (in Ref. 1; AAC50806)"
FT                   /evidence="ECO:0000305"
FT   HELIX           81..96
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   STRAND          106..109
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   HELIX           112..122
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   HELIX           125..130
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   TURN            131..133
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   HELIX           134..140
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   HELIX           149..159
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   HELIX           161..167
FT                   /evidence="ECO:0007829|PDB:2YQE"
FT   STRAND          318..320
FT                   /evidence="ECO:0007829|PDB:2E6R"
FT   HELIX           324..328
FT                   /evidence="ECO:0007829|PDB:2E6R"
FT   TURN            333..335
FT                   /evidence="ECO:0007829|PDB:2E6R"
FT   STRAND          341..346
FT                   /evidence="ECO:0007829|PDB:2E6R"
FT   HELIX           359..366
FT                   /evidence="ECO:0007829|PDB:2E6R"
SQ   SEQUENCE   1539 AA;  174073 MW;  E58DAE374E3BD7AA CRC64;
     MEPGCDEFLP PPECPVFEPS WAEFQDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
     DNFRFTPRVQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLSKIVI
     EEGGYEAICK DRRWARVAQR LHYPPGKNIG SLLRSHYERI IYPYEMFQSG ANHVQCNTHP
     FDNEVKDKEY KPHSIPLRQS VQPSKFSSYS RRAKRLQPDP EPTEEDIEKH PELKKLQIYG
     PGPKMMGLGL MAKDKDKTVH KKVTCPPTVT VKDEQSGGGN VSSTLLKQHL SLEPCTKTTM
     QLRKNHSSAQ FIDSYICQVC SRGDEDDKLL FCDGCDDNYH IFCLLPPLPE IPRGIWRCPK
     CILAECKQPP EAFGFEQATQ EYSLQSFGEM ADSFKSDYFN MPVHMVPTEL VEKEFWRLVS
     SIEEDVTVEY GADIHSKEFG SGFPVSNSKQ NLSPEEKEYA TSGWNLNVMP VLDQSVLCHI
     NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL AAEHLEEVMK
     MLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA YHSGFNQGYN
     FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAAFPETLDL NLAVAVHKEM
     FIMVQEERRL RKALLEKGVT EAEREAFELL PDDERQCIKC KTTCFLSALA CYDCPDGLVC
     LSHINDLCKC SSSRQYLRYR YTLDELPTML HKLKIRAESF DTWANKVRVA LEVEDGRKRS
     FEELRALESE ARERRFPNSE LLQRLKNCLS EVEACIAQVL GLVSGQVARM DTPQLTLTEL
     RVLLEQMGSL PCAMHQIGDV KDVLEQVEAY QAEAREALAT LPSSPGLLRS LLERGQQLGV
     EVPEAHQLQQ QVEQAQWLDE VKQALAPSAH RGSLVIMQGL LVMGAKIASS PSVDKARAEL
     QELLTIAERW EEKAHFCLEA RQKHPPATLE AIIRETENIP VHLPNIQALK EALTKAQAWI
     ADVDEIQNGD HYPCLDDLEG LVAVGRDLPV GLEELRQLEL QVLTAHSWRE KASKTFLKKN
     SCYTLLEVLC PCADAGSDST KRSRWMEKAL GLYQCDTELL GLSAQDLRDP GSVIVAFKEG
     EQKEKEGILQ LRRTNSAKPS PLAPSLMASS PTSICVCGQV PAGVGVLQCD LCQDWFHGQC
     VSVPHLLTSP KPSLTSSPLL AWWEWDTKFL CPLCMRSRRP RLETILALLV ALQRLPVRLP
     EGEALQCLTE RAIGWQDRAR KALASEDVTA LLRQLAELRQ QLQAKPRPEE ASVYTSATAC
     DPIREGSGNN ISKVQGLLEN GDSVTSPENM APGKGSDLEL LSSLLPQLTG PVLELPEAIR
     APLEELMMEG DLLEVTLDEN HSIWQLLQAG QPPDLDRIRT LLELEKFEHQ GSRTRSRALE
     RRRRRQKVDQ GRNVENLVQQ ELQSKRARSS GIMSQVGREE EHYQEKADRE NMFLTPSTDH
     SPFLKGNQNS LQHKDSGSSA ACPSLMPLLQ LSYSDEQQL
//