Q62240

PR
Gene name
Kdm5d (Hya, Jarid1d, Smcy)
Protein name
Lysine-specific demethylase 5D
Names
Histocompatibility Y antigen, H-Y, Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, Protein SmcY, [histone H3]-trimethyl-L-lysine(4) demethylase 5D
Species
Mus musculus (Mouse)
KEGG Pathway
mmu:20592
EC number
1.14.11.67: With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

204-274 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

1 structures for Q62240

Entry ID Method Resolution Chain Position Source
AF-Q62240-F1 Predicted AlphaFoldDB

26 variants for Q62240

Variant ID(s) Position Change Description Diseaes Association Provenance
rs3410013999 26 D>N No EVA
rs3412578230 48 P>S No EVA
rs3412666403 116 N>H No EVA
rs52221093 213 G>A No EVA
rs3412786356 242 G>C No EVA
rs3412666376 244 K>N No EVA
rs3412779249 409 N>S No EVA
rs3411438492 622 L>V No EVA
rs3412579860 623 P>A No EVA
rs3412491472 629 I>V No EVA
rs3412951715 772 W>R No EVA
rs3411438480 788 R>Q No EVA
rs3412694027 804 R>L No EVA
rs3412779325 865 Q>L No EVA
rs3412491621 866 I>F No EVA
rs1132226100 885 E>* No EVA
rs3411440132 977 E>A No EVA
rs3412973315 1057 L>S No EVA
rs3412973280 1152 K>N No EVA
rs3410016455 1229 A>T No EVA
rs3412612413 1248 P>A No EVA
rs3412851113 1248 P>R No EVA
rs3412578980 1274 Q>* No EVA
rs3411440128 1275 C>G No EVA
rs3412973258 1382 G>D No EVA
rs3411900376 1401 E>K No EVA

No associated diseases with Q62240

10 regional properties for Q62240

Type Name Position InterPro Accession
domain ARID DNA-binding domain 79 - 170 IPR001606
domain Zinc finger, PHD-type 325 - 371 IPR001965-1
domain Zinc finger, PHD-type 1182 - 1243 IPR001965-2
domain JmjC domain 467 - 633 IPR003347
domain JmjN domain 13 - 55 IPR003349
domain Zinc finger, C5HC2-type 706 - 758 IPR004198
domain Lysine-specific demethylase-like domain 771 - 1096 IPR013637
conserved_site Zinc finger, PHD-type, conserved site 326 - 370 IPR019786-1
conserved_site Zinc finger, PHD-type, conserved site 1183 - 1242 IPR019786-2
domain Zinc finger, PHD-finger 323 - 373 IPR019787

Functions

Description
EC Number 1.14.11.67 With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
Subcellular Localization
  • Nucleus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

2 GO annotations of cellular component

Name Definition
fibrillar center A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

6 GO annotations of molecular function

Name Definition
DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
histone demethylase activity Catalysis of the removal of a methyl group from a histone.
histone H3-methyl-lysine-4 demethylase activity Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein.
histone H3-tri/di/monomethyl-lysine-4 demethylase activity Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
metal ion binding Binding to a metal ion.
nuclear androgen receptor binding Binding to a nuclear androgen receptor.

4 GO annotations of biological process

Name Definition
chromatin remodeling A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication.
histone H3-K4 demethylation The modification of histone H3 by the removal of a methyl group from lysine at position 4 of the histone.
regulation of androgen receptor signaling pathway Any process that modulates the rate, frequency, or extent of the androgen receptor signaling pathway.
T cell antigen processing and presentation The process in which a T cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.

3 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q9BY66 KDM5D Lysine-specific demethylase 5D Homo sapiens (Human) PR
Q3U2K5 Kdm4d Lysine-specific demethylase 4D Mus musculus (Mouse) PR
Q8BW72 Kdm4a Lysine-specific demethylase 4A Mus musculus (Mouse) PR
10 20 30 40 50 60
MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
70 80 90 100 110 120
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLNKIVM
130 140 150 160 170 180
EEGGYEAICK DRRWARVAQR LNYPSGKNIG SLLRSHYERI IYPYEIFQSG ANLVQCNTDP
190 200 210 220 230 240
FDSEERDKEY KPHSIPLRQS VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG
250 260 270 280 290 300
AGPKMIGLGL KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS
310 320 330 340 350 360
FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI FCLLPPLSEV
370 380 390 400 410 420
PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA DSFKADYFNM PVHMVPTEVV
430 440 450 460 470 480
EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV
490 500 510 520 530 540
LDQSVLCHIN ADISGMKVPW LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA
550 560 570 580 590 600
AEHLEDVMKR LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY
610 620 630 640 650 660
HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM AAFPEKLDLN
670 680 690 700 710 720
LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP DDERQCIKCK TTCFLSALAC
730 740 750 760 770 780
YDCPDSLVCL SHINDLCKCS RNRQYLRYRY TLDELPAMLQ KLKIRAESFD NWANKVQAAL
790 800 810 820 830 840
EVEDGRKRSF EELRALESEA RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ
850 860 870 880 890 900
TPQITLTELQ LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL
910 920 930 940 950 960
MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL VMGTKVASSP
970 980 990 1000 1010 1020
SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV IIREAENIPV YLPNIQSLKE
1030 1040 1050 1060 1070 1080
ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL VAVGRDLPVE LEELRQLENQ VLTAHSWKEK
1090 1100 1110 1120 1130 1140
ASKTFLKKNS CYTLLEVLCP CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG
1150 1160 1170 1180 1190 1200
SVIMAFKEGE EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC
1210 1220 1230 1240 1250 1260
HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL ETILSLLVGL
1270 1280 1290 1300 1310 1320
QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL KQLEKSRQQL QDELRHKKPP
1330 1340 1350 1360 1370 1380
TLPSGFAFDC LTENSGKDIL KEEEELVLNE ERIKSSEKIV PKESSCKGDK ELLPSLLSQL
1390 1400 1410 1420 1430 1440
TGPVLELPEA TRAPLEELMM EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE
1450 1460 1470 1480 1490 1500
NPGNWSEEQT PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN
1510 1520 1530 1540
VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL