UniProtKB - Q62240 (KDM5D_MOUSE)
Protein
Lysine-specific demethylase 5D
Gene
Kdm5d
Organism
Mus musculus (Mouse)
Status
Functioni
Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks (By similarity).By similarity2 Publications
Miscellaneous
KDM5D encodes an H-Y epitope that is defined by the octamer peptide TENSGKDI; since no similar peptide was found in KDM5C, it is presumably the genetic basis for the antigenic difference between males and females that contributes toward a tissue transplant rejection response.
Catalytic activityi
- 3 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl4-[histone H3] + 3 succinateBy similarityEC:1.14.11.67By similarity
Cofactori
Protein has several cofactor binding sites:- L-ascorbateBy similarity
- Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 439 | 2-oxoglutarateBy similarity | 1 | |
Metal bindingi | 513 | Iron; catalyticPROSITE-ProRule annotation | 1 | |
Metal bindingi | 515 | Iron; catalyticBy similarity | 1 | |
Binding sitei | 521 | 2-oxoglutarateBy similarity | 1 | |
Binding sitei | 523 | 2-oxoglutarateBy similarity | 1 | |
Binding sitei | 531 | 2-oxoglutarateBy similarity | 1 | |
Metal bindingi | 601 | Iron; catalyticPROSITE-ProRule annotation | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 325 – 371 | PHD-type 1PROSITE-ProRule annotationAdd BLAST | 47 | |
Zinc fingeri | 706 – 758 | C5HC2By similarityAdd BLAST | 53 | |
Zinc fingeri | 1182 – 1243 | PHD-type 2PROSITE-ProRule annotationAdd BLAST | 62 |
GO - Molecular functioni
- androgen receptor binding Source: MGI
- dioxygenase activity Source: UniProtKB-KW
- DNA binding Source: InterPro
- histone demethylase activity Source: GO_Central
- histone demethylase activity (H3-K4 specific) Source: MGI
- histone demethylase activity (H3-trimethyl-K4 specific) Source: GO_Central
- metal ion binding Source: UniProtKB-KW
GO - Biological processi
- chromatin remodeling Source: GO_Central
- histone H3-K4 demethylation Source: MGI
- regulation of androgen receptor signaling pathway Source: MGI
- T cell antigen processing and presentation Source: MGI
Keywordsi
Molecular function | Chromatin regulator, Dioxygenase, Oxidoreductase |
Biological process | Transcription, Transcription regulation |
Ligand | Iron, Metal-binding, Zinc |
Names & Taxonomyi
Protein namesi | Recommended name: Lysine-specific demethylase 5D (EC:1.14.11.67By similarity)Alternative name(s): Histocompatibility Y antigen Short name: H-Y Histone demethylase JARID1D Jumonji/ARID domain-containing protein 1D Protein SmcY [histone H3]-trimethyl-L-lysine(4) demethylase 5DCurated |
Gene namesi | Name:Kdm5d Synonyms:Hya, Jarid1d, Smcy |
Organismi | Mus musculus (Mouse) |
Taxonomic identifieri | 10090 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus |
Proteomesi |
|
Organism-specific databases
MGIi | MGI:99780, Kdm5d |
Subcellular locationi
Nucleus
- Nucleus PROSITE-ProRule annotationBy similarity
Nucleus
- fibrillar center Source: MGI
- histone methyltransferase complex Source: GO_Central
- nucleus Source: GO_Central
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000200589 | 1 – 1548 | Lysine-specific demethylase 5DAdd BLAST | 1548 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 205 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Cross-linki | 229 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Cross-linki | 244 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Cross-linki | 279 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Modified residuei | 300 | PhosphoserineBy similarity | 1 | |
Modified residuei | 316 | PhosphoserineBy similarity | 1 | |
Modified residuei | 889 | PhosphoserineBy similarity | 1 | |
Modified residuei | 893 | PhosphoserineBy similarity | 1 | |
Cross-linki | 1123 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Modified residuei | 1355 | PhosphoserineBy similarity | 1 |
Keywords - PTMi
Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q62240 |
PaxDbi | Q62240 |
PeptideAtlasi | Q62240 |
PRIDEi | Q62240 |
PTM databases
iPTMneti | Q62240 |
PhosphoSitePlusi | Q62240 |
Expressioni
Gene expression databases
Bgeei | ENSMUSG00000056673, Expressed in undifferentiated genital tubercle and 240 other tissues |
ExpressionAtlasi | Q62240, baseline and differential |
Genevisiblei | Q62240, MM |
Interactioni
Subunit structurei
Interacts withPCGF6, MSH5, ZMYND8, AR.
By similarityGO - Molecular functioni
- androgen receptor binding Source: MGI
Protein-protein interaction databases
BioGRIDi | 203342, 5 interactors |
STRINGi | 10090.ENSMUSP00000061095 |
Miscellaneous databases
RNActi | Q62240, protein |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 14 – 55 | JmjNPROSITE-ProRule annotationAdd BLAST | 42 | |
Domaini | 79 – 169 | ARIDPROSITE-ProRule annotationAdd BLAST | 91 | |
Domaini | 467 – 633 | JmjCPROSITE-ProRule annotationAdd BLAST | 167 |
Domaini
The JmjC domain is required for enzymatic activity.By similarity
Sequence similaritiesi
Belongs to the JARID1 histone demethylase family.Curated
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 325 – 371 | PHD-type 1PROSITE-ProRule annotationAdd BLAST | 47 | |
Zinc fingeri | 706 – 758 | C5HC2By similarityAdd BLAST | 53 | |
Zinc fingeri | 1182 – 1243 | PHD-type 2PROSITE-ProRule annotationAdd BLAST | 62 |
Keywords - Domaini
Repeat, Zinc-fingerPhylogenomic databases
eggNOGi | KOG1246, Eukaryota |
GeneTreei | ENSGT00940000161236 |
HOGENOMi | CLU_000991_2_2_1 |
InParanoidi | Q62240 |
OMAi | CECPPEN |
OrthoDBi | 664180at2759 |
PhylomeDBi | Q62240 |
TreeFami | TF106476 |
Family and domain databases
Gene3Di | 1.10.150.60, 1 hit 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR001606, ARID_dom IPR036431, ARID_dom_sf IPR003347, JmjC_dom IPR003349, JmjN IPR013637, Lys_sp_deMease-like_dom IPR019786, Zinc_finger_PHD-type_CS IPR004198, Znf_C5HC2 IPR011011, Znf_FYVE_PHD IPR001965, Znf_PHD IPR019787, Znf_PHD-finger IPR013083, Znf_RING/FYVE/PHD |
Pfami | View protein in Pfam PF01388, ARID, 1 hit PF02373, JmjC, 1 hit PF02375, JmjN, 1 hit PF00628, PHD, 1 hit PF08429, PLU-1, 1 hit PF02928, zf-C5HC2, 1 hit |
SMARTi | View protein in SMART SM00501, BRIGHT, 1 hit SM00558, JmjC, 1 hit SM00545, JmjN, 1 hit SM00249, PHD, 2 hits |
SUPFAMi | SSF46774, SSF46774, 1 hit SSF57903, SSF57903, 2 hits |
PROSITEi | View protein in PROSITE PS51011, ARID, 1 hit PS51184, JMJC, 1 hit PS51183, JMJN, 1 hit PS01359, ZF_PHD_1, 2 hits PS50016, ZF_PHD_2, 1 hit |
s (4+)i Sequence
Sequence statusi: Complete.
This entry describes 4 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 4 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All
Isoform 1 (identifier: Q62240-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA
60 70 80 90 100
DWQPPFAVEV DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL
110 120 130 140 150
KIPNVERKIL DLYSLNKIVM EEGGYEAICK DRRWARVAQR LNYPSGKNIG
160 170 180 190 200
SLLRSHYERI IYPYEIFQSG ANLVQCNTDP FDSEERDKEY KPHSIPLRQS
210 220 230 240 250
VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG AGPKMIGLGL
260 270 280 290 300
KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS
310 320 330 340 350
FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI
360 370 380 390 400
FCLLPPLSEV PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA
410 420 430 440 450
DSFKADYFNM PVHMVPTEVV EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS
460 470 480 490 500
GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV LDQSVLCHIN ADISGMKVPW
510 520 530 540 550
LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA AEHLEDVMKR
560 570 580 590 600
LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY
610 620 630 640 650
HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM
660 670 680 690 700
AAFPEKLDLN LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP
710 720 730 740 750
DDERQCIKCK TTCFLSALAC YDCPDSLVCL SHINDLCKCS RNRQYLRYRY
760 770 780 790 800
TLDELPAMLQ KLKIRAESFD NWANKVQAAL EVEDGRKRSF EELRALESEA
810 820 830 840 850
RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ TPQITLTELQ
860 870 880 890 900
LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL
910 920 930 940 950
MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL
960 970 980 990 1000
VMGTKVASSP SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV
1010 1020 1030 1040 1050
IIREAENIPV YLPNIQSLKE ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL
1060 1070 1080 1090 1100
VAVGRDLPVE LEELRQLENQ VLTAHSWKEK ASKTFLKKNS CYTLLEVLCP
1110 1120 1130 1140 1150
CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG SVIMAFKEGE
1160 1170 1180 1190 1200
EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC
1210 1220 1230 1240 1250
HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL
1260 1270 1280 1290 1300
ETILSLLVGL QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL
1310 1320 1330 1340 1350
KQLEKSRQQL QDELRHKKPP TLPSGFAFDC LTENSGKDIL KEEEELVLNE
1360 1370 1380 1390 1400
ERIKSSEKIV PKESSCKGDK ELLPSLLSQL TGPVLELPEA TRAPLEELMM
1410 1420 1430 1440 1450
EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE NPGNWSEEQT
1460 1470 1480 1490 1500
PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN
1510 1520 1530 1540
VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL
Isoform 4 (identifier: Q62240-4) [UniParc]FASTAAdd to basket
The sequence of this isoform differs from the canonical sequence as follows:
687-691: GITEA → LSLQA
692-1548: Missing.
Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.Curated
Show »Computationally mapped potential isoform sequencesi
There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketQ8BQM3 | Q8BQM3_MOUSE | [Histone H3]-trimethyl-L-lysine(4) ... | Kdm5d Jarid1d | 476 | Annotation score: | ||
A0A087WR43 | A0A087WR43_MOUSE | Lysine-specific demethylase 5D | Kdm5d | 271 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 160 – 162 | IIY → SFT in CAA82760 (PubMed:7524912).Curated | 3 | |
Sequence conflicti | 167 | F → S in CAA82760 (PubMed:7524912).Curated | 1 | |
Sequence conflicti | 215 | R → K in CAA82760 (PubMed:7524912).Curated | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_026412 | 1 – 398 | Missing in isoform 2. 1 PublicationAdd BLAST | 398 | |
Alternative sequenceiVSP_026413 | 583 – 586 | VRTN → SIWK in isoform 3. 1 Publication | 4 | |
Alternative sequenceiVSP_026414 | 587 – 1548 | Missing in isoform 3. 1 PublicationAdd BLAST | 962 | |
Alternative sequenceiVSP_026415 | 687 – 691 | GITEA → LSLQA in isoform 4. 1 Publication | 5 | |
Alternative sequenceiVSP_026416 | 692 – 1548 | Missing in isoform 4. 1 PublicationAdd BLAST | 857 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF127244 mRNA Translation: AAD53048.1 AK140971 mRNA Translation: BAE24534.1 BC059077 mRNA Translation: AAH59077.1 Z29652 mRNA Translation: CAA82760.1 |
CCDSi | CCDS30541.1 [Q62240-1] |
PIRi | I48776 |
RefSeqi | NP_035549.1, NM_011419.3 [Q62240-1] |
Genome annotation databases
Ensembli | ENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673 [Q62240-1] ENSMUST00000186696; ENSMUSP00000140663; ENSMUSG00000056673 [Q62240-4] |
GeneIDi | 20592 |
KEGGi | mmu:20592 |
UCSCi | uc009uyz.1, mouse [Q62240-3] uc009uzb.1, mouse [Q62240-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF127244 mRNA Translation: AAD53048.1 AK140971 mRNA Translation: BAE24534.1 BC059077 mRNA Translation: AAH59077.1 Z29652 mRNA Translation: CAA82760.1 |
CCDSi | CCDS30541.1 [Q62240-1] |
PIRi | I48776 |
RefSeqi | NP_035549.1, NM_011419.3 [Q62240-1] |
3D structure databases
SMRi | Q62240 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 203342, 5 interactors |
STRINGi | 10090.ENSMUSP00000061095 |
PTM databases
iPTMneti | Q62240 |
PhosphoSitePlusi | Q62240 |
Proteomic databases
EPDi | Q62240 |
PaxDbi | Q62240 |
PeptideAtlasi | Q62240 |
PRIDEi | Q62240 |
Protocols and materials databases
Antibodypediai | 21879, 43 antibodies |
Genome annotation databases
Ensembli | ENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673 [Q62240-1] ENSMUST00000186696; ENSMUSP00000140663; ENSMUSG00000056673 [Q62240-4] |
GeneIDi | 20592 |
KEGGi | mmu:20592 |
UCSCi | uc009uyz.1, mouse [Q62240-3] uc009uzb.1, mouse [Q62240-1] |
Organism-specific databases
CTDi | 8284 |
MGIi | MGI:99780, Kdm5d |
Phylogenomic databases
eggNOGi | KOG1246, Eukaryota |
GeneTreei | ENSGT00940000161236 |
HOGENOMi | CLU_000991_2_2_1 |
InParanoidi | Q62240 |
OMAi | CECPPEN |
OrthoDBi | 664180at2759 |
PhylomeDBi | Q62240 |
TreeFami | TF106476 |
Miscellaneous databases
BioGRID-ORCSi | 20592, 0 hits in 19 CRISPR screens |
ChiTaRSi | Kdm5d, mouse |
PROi | PR:Q62240 |
RNActi | Q62240, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSMUSG00000056673, Expressed in undifferentiated genital tubercle and 240 other tissues |
ExpressionAtlasi | Q62240, baseline and differential |
Genevisiblei | Q62240, MM |
Family and domain databases
Gene3Di | 1.10.150.60, 1 hit 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR001606, ARID_dom IPR036431, ARID_dom_sf IPR003347, JmjC_dom IPR003349, JmjN IPR013637, Lys_sp_deMease-like_dom IPR019786, Zinc_finger_PHD-type_CS IPR004198, Znf_C5HC2 IPR011011, Znf_FYVE_PHD IPR001965, Znf_PHD IPR019787, Znf_PHD-finger IPR013083, Znf_RING/FYVE/PHD |
Pfami | View protein in Pfam PF01388, ARID, 1 hit PF02373, JmjC, 1 hit PF02375, JmjN, 1 hit PF00628, PHD, 1 hit PF08429, PLU-1, 1 hit PF02928, zf-C5HC2, 1 hit |
SMARTi | View protein in SMART SM00501, BRIGHT, 1 hit SM00558, JmjC, 1 hit SM00545, JmjN, 1 hit SM00249, PHD, 2 hits |
SUPFAMi | SSF46774, SSF46774, 1 hit SSF57903, SSF57903, 2 hits |
PROSITEi | View protein in PROSITE PS51011, ARID, 1 hit PS51184, JMJC, 1 hit PS51183, JMJN, 1 hit PS01359, ZF_PHD_1, 2 hits PS50016, ZF_PHD_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | KDM5D_MOUSE | |
Accessioni | Q62240Primary (citable) accession number: Q62240 Secondary accession number(s): Q3US03 Q9R040 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 24, 2001 |
Last sequence update: | October 24, 2001 | |
Last modified: | December 2, 2020 | |
This is version 162 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- MGD cross-references
Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot - SIMILARITY comments
Index of protein domains and families