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 27-MAR-2024, entry version 197.
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};
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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; 7.
DR IntAct; Q9BY66; 5.
DR STRING; 9606.ENSP00000322408; -.
DR BindingDB; Q9BY66; -.
DR ChEMBL; CHEMBL5169191; -.
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 PeptideAtlas; Q9BY66; -.
DR ProteomicsDB; 79591; -. [Q9BY66-1]
DR ProteomicsDB; 79592; -. [Q9BY66-2]
DR ProteomicsDB; 79593; -. [Q9BY66-3]
DR Pumba; Q9BY66; -.
DR ABCD; Q9BY66; 1 sequenced antibody.
DR Antibodypedia; 21879; 61 antibodies from 26 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 AGR; HGNC:11115; -.
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; SAVNCKC; -.
DR OrthoDB; 48111at2759; -.
DR PhylomeDB; Q9BY66; -.
DR TreeFam; TF106476; -.
DR BioCyc; MetaCyc:ENSG00000012817-MONOMER; -.
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; 14 hits in 807 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 190 other cell types or tissues.
DR ExpressionAtlas; Q9BY66; baseline and differential.
DR Genevisible; Q9BY66; HS.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
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; TAS:Reactome.
DR GO; GO:0032453; F:histone H3K4 demethylase activity; IDA:MGI.
DR GO; GO:0034647; F:histone H3K4me/H3K4me2/H3K4me3 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:0060765; P:regulation of androgen receptor signaling pathway; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of DNA-templated transcription; IBA:GO_Central.
DR GO; GO:0002457; P:T cell antigen processing and presentation; IEA:Ensembl.
DR CDD; cd16875; ARID_KDM5C_5D; 1.
DR CDD; cd15604; PHD1_KDM5C_5D; 1.
DR CDD; cd15608; PHD2_KDM5C_5D; 1.
DR Gene3D; 1.10.150.60; ARID DNA-binding domain; 1.
DR Gene3D; 2.60.120.650; Cupin; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 2.
DR InterPro; IPR001606; ARID_dom.
DR InterPro; IPR036431; ARID_dom_sf.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR048615; KDM5_C-hel.
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 PANTHER; PTHR10694; LYSINE-SPECIFIC DEMETHYLASE; 1.
DR PANTHER; PTHR10694:SF84; LYSINE-SPECIFIC DEMETHYLASE 5D; 1.
DR Pfam; PF01388; ARID; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF21323; KDM5_C-hel; 1.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF08429; PLU-1; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM01014; ARID; 1.
DR SMART; SM00501; BRIGHT; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 2.
DR SUPFAM; SSF46774; ARID-like; 1.
DR SUPFAM; SSF51197; Clavaminate synthase-like; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 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
//
