KDM4D_MOUSE
ID KDM4D_MOUSE Reviewed; 510 AA.
AC Q3U2K5; A2CGB5; B8JK34; Q2M1G7; Q8BI19;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 2.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Lysine-specific demethylase 4D;
DE EC=1.14.11.66 {ECO:0000250|UniProtKB:Q6B0I6};
DE AltName: Full=JmjC domain-containing histone demethylation protein 3D;
DE AltName: Full=Jumonji domain-containing protein 2D;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(9) demethylase 4D {ECO:0000305};
GN Name=Kdm4d; Synonyms=Jhdm3d, Jmjd2d;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J, and NOD; TISSUE=Testis;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 106-510.
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).
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of
CC histone H3, thereby playing a central role in histone code. Does not
CC demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-
CC 20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while
CC it has no activity on monomethylated residues. Demethylation of Lys
CC residue generates formaldehyde and succinate.
CC {ECO:0000250|UniProtKB:Q6B0I6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-
CC [histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L-
CC lysyl(9)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60200, Rhea:RHEA-
CC COMP:15538, Rhea:RHEA-COMP:15542, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, ChEBI:CHEBI:61961;
CC EC=1.14.11.66; Evidence={ECO:0000250|UniProtKB:Q6B0I6};
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:0000255|PROSITE-ProRule:PRU00537}.
CC -!- SIMILARITY: Belongs to the JHDM3 histone demethylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC26740.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAC26740.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=BAE33135.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AK030020; BAC26740.1; ALT_SEQ; mRNA.
DR EMBL; AK155227; BAE33135.1; ALT_FRAME; mRNA.
DR EMBL; CT485607; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC112372; AAI12373.1; -; mRNA.
DR CCDS; CCDS22822.2; -.
DR RefSeq; NP_775609.2; NM_173433.2.
DR RefSeq; XP_006510333.1; XM_006510270.2.
DR RefSeq; XP_006510334.1; XM_006510271.2.
DR AlphaFoldDB; Q3U2K5; -.
DR SMR; Q3U2K5; -.
DR BioGRID; 232681; 3.
DR STRING; 10090.ENSMUSP00000061632; -.
DR PhosphoSitePlus; Q3U2K5; -.
DR PaxDb; Q3U2K5; -.
DR PRIDE; Q3U2K5; -.
DR ProteomicsDB; 263523; -.
DR Antibodypedia; 17907; 250 antibodies from 32 providers.
DR DNASU; 244694; -.
DR Ensembl; ENSMUST00000058796; ENSMUSP00000061632; ENSMUSG00000053914.
DR GeneID; 244694; -.
DR KEGG; mmu:244694; -.
DR UCSC; uc009oen.1; mouse.
DR CTD; 55693; -.
DR MGI; MGI:3606484; Kdm4d.
DR VEuPathDB; HostDB:ENSMUSG00000053914; -.
DR eggNOG; KOG0958; Eukaryota.
DR GeneTree; ENSGT00940000162152; -.
DR InParanoid; Q3U2K5; -.
DR OMA; RASICKC; -.
DR OrthoDB; 1186832at2759; -.
DR PhylomeDB; Q3U2K5; -.
DR TreeFam; TF106449; -.
DR BRENDA; 1.14.11.66; 3474.
DR BRENDA; 1.14.11.B19; 3474.
DR Reactome; R-MMU-3214842; HDMs demethylate histones.
DR BioGRID-ORCS; 244694; 4 hits in 111 CRISPR screens.
DR PRO; PR:Q3U2K5; -.
DR Proteomes; UP000000589; Chromosome 9.
DR RNAct; Q3U2K5; protein.
DR Bgee; ENSMUSG00000053914; Expressed in spermatocyte and 19 other tissues.
DR ExpressionAtlas; Q3U2K5; baseline and differential.
DR Genevisible; Q3U2K5; MM.
DR GO; GO:0005634; C:nucleus; IDA:MGI.
DR GO; GO:0005721; C:pericentric heterochromatin; IDA:MGI.
DR GO; GO:0035861; C:site of double-strand break; IDA:MGI.
DR GO; GO:0031490; F:chromatin DNA binding; IDA:MGI.
DR GO; GO:0003684; F:damaged DNA binding; IDA:MGI.
DR GO; GO:0032452; F:histone demethylase activity; IDA:MGI.
DR GO; GO:0032454; F:histone H3-methyl-lysine-9 demethylase activity; IMP:MGI.
DR GO; GO:0140684; F:histone H3-tri/dimethyl-lysine-9 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:MGI.
DR GO; GO:0071479; P:cellular response to ionizing radiation; ISO:MGI.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0000724; P:double-strand break repair via homologous recombination; ISO:MGI.
DR GO; GO:0033169; P:histone H3-K9 demethylation; IDA:MGI.
DR GO; GO:1900113; P:negative regulation of histone H3-K9 trimethylation; IDA:MGI.
DR GO; GO:0035563; P:positive regulation of chromatin binding; ISO:MGI.
DR GO; GO:2001034; P:positive regulation of double-strand break repair via nonhomologous end joining; ISO:MGI.
DR GO; GO:0001932; P:regulation of protein phosphorylation; ISO:MGI.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
PE 2: Evidence at transcript level;
KW ADP-ribosylation; Chromatin regulator; Dioxygenase; Iron; Metal-binding;
KW Nucleus; Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc.
FT CHAIN 1..510
FT /note="Lysine-specific demethylase 4D"
FT /id="PRO_0000234377"
FT DOMAIN 15..57
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 143..309
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT REGION 397..510
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 419..436
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 133
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 189
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 191
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 199
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 207
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 235
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q6B0I6"
FT BINDING 241
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q6B0I6"
FT BINDING 242
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:B2RXH2"
FT BINDING 277
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 307
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q6B0I6"
FT BINDING 309
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q6B0I6"
FT MOD_RES 23
FT /note="PolyADP-ribosyl glutamic acid"
FT /evidence="ECO:0000250"
FT MOD_RES 24
FT /note="PolyADP-ribosyl glutamic acid"
FT /evidence="ECO:0000250"
FT CONFLICT 374
FT /note="R -> L (in Ref. 1; BAC26740)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 510 AA; 57212 MW; 6B57A0300BAD94C9 CRC64;
MKTKSTCAQN PNCSIMIFRP TKEEFNDFDK YIAYMESQGA HRAGLAKVIP PKEWRARQSY
DNISNILIAT PLQQVVSGQA GVFTQYHKKK KGMTVGEYRE LANSKKYQTP PHLDFEDLER
KYWKNRLYES PIYGADVSGS LFDGKTQQWN VGHLGTIQDL LEQECGIVIE GVNTPYLYFG
MWKTTFAWHT EDMDLYSINY LHFGQPKTWY AVPPEHGRRL ERLARELFPG SSQGCQAFLR
HKVALISPTV LKENGIPFGR ITQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
GKVASQCSCG EARVSFSMDA FVRILQPERY ELWKRGQDQA VVDHTETMVS TSQELTTRRV
TKAPRKTWGL KRLRLRQVSR SLLPIATVSN VPCNMQVCHT SRQPSDVKGD DVQKSDSARA
SPHPLSLPSS GHMSTRRCSL GRRPCELGAQ ESSNGAPVKR QLPAGRDDTS PSPELQPQAV
SGDLIVDSGL VNPGPQHLMT ASEGGLTSDP
