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Q62240

- KDM5D_MOUSE

UniProt

Q62240 - KDM5D_MOUSE

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Protein
Lysine-specific demethylase 5D
Gene
Kdm5d, Hya, Jarid1d, Smcy
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at transcript leveli

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 By similarity.2 Publications

Cofactori

Ascorbate By similarity.
Binds 1 Fe2+ ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi513 – 5131Iron; catalytic By similarity
Metal bindingi516 – 5161Iron; catalytic By similarity
Metal bindingi601 – 6011Iron; catalytic By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri325 – 37147PHD-type 1
Add
BLAST
Zinc fingeri1182 – 124362PHD-type 2
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. histone demethylase activity (H3-K4 specific) Source: Ensembl
  3. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: InterPro
  4. zinc ion binding Source: InterPro
Complete GO annotation...

GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lysine-specific demethylase 5D (EC:1.14.11.-)
    Alternative name(s):
    Histocompatibility Y antigen
    Short name:
    H-Y
    Histone demethylase JARID1D
    Jumonji/ARID domain-containing protein 1D
    Protein SmcY
    Gene namesi
    Name:Kdm5d
    Synonyms:Hya, Jarid1d, Smcy
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome Y

    Organism-specific databases

    MGIiMGI:99780. Kdm5d.

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 15481548Lysine-specific demethylase 5D
    PRO_0000200589Add
    BLAST

    Proteomic databases

    PaxDbiQ62240.
    PRIDEiQ62240.

    PTM databases

    PhosphoSiteiQ62240.

    Expressioni

    Gene expression databases

    BgeeiQ62240.
    GenevestigatoriQ62240.

    Interactioni

    Subunit structurei

    Interacts with PCGF6 and MSH5 By similarity.

    Protein-protein interaction databases

    BioGridi203342. 3 interactions.
    STRINGi10090.ENSMUSP00000061095.

    Structurei

    3D structure databases

    ProteinModelPortaliQ62240.
    SMRiQ62240. Positions 13-76, 79-171, 319-659, 1179-1248.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini14 – 5542JmjN
    Add
    BLAST
    Domaini79 – 16991ARID
    Add
    BLAST
    Domaini467 – 633167JmjC
    Add
    BLAST

    Domaini

    The JmjC domain is required for enzymatic activity By similarity.

    Sequence similaritiesi

    Contains 1 ARID domain.
    Contains 1 JmjC domain.
    Contains 1 JmjN domain.

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiNOG327026.
    GeneTreeiENSGT00530000063118.
    HOGENOMiHOG000290719.
    InParanoidiQ62240.
    KOiK11446.
    OMAiILMNANV.
    OrthoDBiEOG7D85VK.
    PhylomeDBiQ62240.
    TreeFamiTF106476.

    Family and domain databases

    Gene3Di1.10.150.60. 1 hit.
    3.30.40.10. 2 hits.
    InterProiIPR001606. ARID/BRIGHT_DNA-bd.
    IPR003347. JmjC_dom.
    IPR013637. Lys_sp_deMease_like_dom.
    IPR003349. TF_JmjN.
    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.
    [Graphical view]
    PfamiPF01388. 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.
    [Graphical view]
    SMARTiSM00501. BRIGHT. 1 hit.
    SM00558. JmjC. 1 hit.
    SM00545. JmjN. 1 hit.
    SM00249. PHD. 2 hits.
    [Graphical view]
    SUPFAMiSSF46774. SSF46774. 1 hit.
    SSF57903. SSF57903. 2 hits.
    PROSITEiPS51011. ARID. 1 hit.
    PS51184. JMJC. 1 hit.
    PS51183. JMJN. 1 hit.
    PS01359. ZF_PHD_1. 2 hits.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q62240-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA     50
    DWQPPFAVEV DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL 100
    KIPNVERKIL DLYSLNKIVM EEGGYEAICK DRRWARVAQR LNYPSGKNIG 150
    SLLRSHYERI IYPYEIFQSG ANLVQCNTDP FDSEERDKEY KPHSIPLRQS 200
    VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG AGPKMIGLGL 250
    KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS 300
    FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI 350
    FCLLPPLSEV PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA 400
    DSFKADYFNM PVHMVPTEVV EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS 450
    GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV LDQSVLCHIN ADISGMKVPW 500
    LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA AEHLEDVMKR 550
    LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY 600
    HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM 650
    AAFPEKLDLN LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP 700
    DDERQCIKCK TTCFLSALAC YDCPDSLVCL SHINDLCKCS RNRQYLRYRY 750
    TLDELPAMLQ KLKIRAESFD NWANKVQAAL EVEDGRKRSF EELRALESEA 800
    RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ TPQITLTELQ 850
    LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL 900
    MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL 950
    VMGTKVASSP SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV 1000
    IIREAENIPV YLPNIQSLKE ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL 1050
    VAVGRDLPVE LEELRQLENQ VLTAHSWKEK ASKTFLKKNS CYTLLEVLCP 1100
    CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG SVIMAFKEGE 1150
    EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC 1200
    HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL 1250
    ETILSLLVGL QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL 1300
    KQLEKSRQQL QDELRHKKPP TLPSGFAFDC LTENSGKDIL KEEEELVLNE 1350
    ERIKSSEKIV PKESSCKGDK ELLPSLLSQL TGPVLELPEA TRAPLEELMM 1400
    EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE NPGNWSEEQT 1450
    PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN 1500
    VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL 1548
    Length:1,548
    Mass (Da):177,018
    Last modified:October 24, 2001 - v2
    Checksum:i44AAB94708EA4A02
    GO
    Isoform 2 (identifier: Q62240-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-398: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:1,150
    Mass (Da):131,396
    Checksum:i2920BEB66B2E98CF
    GO
    Isoform 3 (identifier: Q62240-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         583-586: VRTN → SIWK
         587-1548: Missing.

    Note: May be due to an intron retention. No experimental confirmation available.

    Show »
    Length:586
    Mass (Da):67,244
    Checksum:iA5764F58390D60F8
    GO
    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: No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Show »
    Length:691
    Mass (Da):79,525
    Checksum:i40681B920A8B54FE
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 398398Missing in isoform 2.
    VSP_026412Add
    BLAST
    Alternative sequencei583 – 5864VRTN → SIWK in isoform 3.
    VSP_026413
    Alternative sequencei587 – 1548962Missing in isoform 3.
    VSP_026414Add
    BLAST
    Alternative sequencei687 – 6915GITEA → LSLQA in isoform 4.
    VSP_026415
    Alternative sequencei692 – 1548857Missing in isoform 4.
    VSP_026416Add
    BLAST

    Sequence conflict

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti160 – 1623IIY → SFT in CAA82760. 1 Publication
    Sequence conflicti167 – 1671F → S in CAA82760. 1 Publication
    Sequence conflicti215 – 2151R → K in CAA82760. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF127244 mRNA. Translation: AAD53048.1.
    AK140971 mRNA. Translation: BAE24534.1.
    BC059077 mRNA. Translation: AAH59077.1.
    Z29652 mRNA. Translation: CAA82760.1.
    CCDSiCCDS30541.1. [Q62240-1]
    PIRiI48776.
    RefSeqiNP_035549.1. NM_011419.3. [Q62240-1]
    UniGeneiMm.262676.

    Genome annotation databases

    EnsembliENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673. [Q62240-1]
    GeneIDi20592.
    KEGGimmu:20592.
    UCSCiuc009uyz.1. mouse. [Q62240-3]
    uc009uzb.1. mouse. [Q62240-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 ]
    UniGenei Mm.262676.

    3D structure databases

    ProteinModelPortali Q62240.
    SMRi Q62240. Positions 13-76, 79-171, 319-659, 1179-1248.
    ModBasei Search...

    Protein-protein interaction databases

    BioGridi 203342. 3 interactions.
    STRINGi 10090.ENSMUSP00000061095.

    PTM databases

    PhosphoSitei Q62240.

    Proteomic databases

    PaxDbi Q62240.
    PRIDEi Q62240.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000055032 ; ENSMUSP00000061095 ; ENSMUSG00000056673 . [Q62240-1 ]
    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 NOG327026.
    GeneTreei ENSGT00530000063118.
    HOGENOMi HOG000290719.
    InParanoidi Q62240.
    KOi K11446.
    OMAi ILMNANV.
    OrthoDBi EOG7D85VK.
    PhylomeDBi Q62240.
    TreeFami TF106476.

    Miscellaneous databases

    NextBioi 298905.
    PROi Q62240.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q62240.
    Genevestigatori Q62240.

    Family and domain databases

    Gene3Di 1.10.150.60. 1 hit.
    3.30.40.10. 2 hits.
    InterProi IPR001606. ARID/BRIGHT_DNA-bd.
    IPR003347. JmjC_dom.
    IPR013637. Lys_sp_deMease_like_dom.
    IPR003349. TF_JmjN.
    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.
    [Graphical view ]
    Pfami 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.
    [Graphical view ]
    SMARTi SM00501. BRIGHT. 1 hit.
    SM00558. JmjC. 1 hit.
    SM00545. JmjN. 1 hit.
    SM00249. PHD. 2 hits.
    [Graphical view ]
    SUPFAMi SSF46774. SSF46774. 1 hit.
    SSF57903. SSF57903. 2 hits.
    PROSITEi PS51011. ARID. 1 hit.
    PS51184. JMJC. 1 hit.
    PS51183. JMJN. 1 hit.
    PS01359. ZF_PHD_1. 2 hits.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    « Hide 'large scale' publications
    1. "Mouse H-Y encoding Smcy gene and its X chromosomal homolog Smcx."
      Agulnik A.I., Longepied G., Ty M.T., Bishop C.E., Mitchell M.J.
      Mamm. Genome 10:926-929(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Strain: 129/SvJ.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
      Strain: C57BL/6J.
      Tissue: Head.
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Strain: C57BL/6.
      Tissue: Brain.
    4. "A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens."
      Agulnik A.I., Mitchell M.J., Lerner J.L., Woods D.R., Bishop C.E.
      Hum. Mol. Genet. 3:873-878(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 23-1548 (ISOFORM 3).
      Strain: BALB/c.
      Tissue: Testis.
    5. "Identification of a mouse male-specific transplantation antigen, H-Y."
      Scott D.M., Ehrmann I.E., Ellis P.S., Bishop C.E., Agulnik A.I., Simpson E., Mitchell M.J.
      Nature 376:695-698(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Spermatogenic failure in male mice lacking H-Y antigen."
      Burgoyne P.S., Levy E.R., McLaren A.
      Nature 320:170-172(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiKDM5D_MOUSE
    AccessioniPrimary (citable) accession number: Q62240
    Secondary accession number(s): Q3US03
    , Q6PCX3, Q9QVR9, Q9R040
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 24, 2001
    Last sequence update: October 24, 2001
    Last modified: July 9, 2014
    This is version 118 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    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.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi