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Protein

Lysine-specific demethylase 7A

Gene

KDM7A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate.3 Publications

Cofactori

Fe2+2 PublicationsNote: Binds 1 Fe2+ ion per subunit.2 Publications

Kineticsi

  1. KM=1.2 µM for histone H3 H3K9Me21 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei279SubstrateBy similarity1
    Metal bindingi282Iron; catalyticPROSITE-ProRule annotation1 Publication1
    Metal bindingi284Iron; catalyticPROSITE-ProRule annotation1 Publication1
    Binding sitei299SubstrateBy similarity1
    Metal bindingi354Iron; catalyticPROSITE-ProRule annotation1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri37 – 88PHD-typePROSITE-ProRule annotationAdd BLAST52

    GO - Molecular functioni

    • histone demethylase activity Source: Reactome
    • histone demethylase activity (H3-K27 specific) Source: UniProtKB
    • histone demethylase activity (H3-K36 specific) Source: UniProtKB
    • histone demethylase activity (H3-K9 specific) Source: UniProtKB
    • histone demethylase activity (H4-K20 specific) Source: UniProtKB
    • iron ion binding Source: UniProtKB
    • methylated histone binding Source: UniProtKB
    • 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: UniProtKB
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • histone H3-K27 demethylation Source: UniProtKB
    • histone H3-K36 demethylation Source: UniProtKB
    • histone H3-K9 demethylation Source: UniProtKB
    • histone H4-K20 demethylation Source: UniProtKB
    • midbrain development Source: UniProtKB
    • positive regulation of transcription, DNA-templated Source: Ensembl
    • transcription, DNA-templated Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Neurogenesis, Transcription, Transcription regulation

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiR-HSA-3214842. HDMs demethylate histones.
    R-HSA-6802952. Signaling by BRAF and RAF fusions.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lysine-specific demethylase 7A (EC:1.14.11.-)
    Alternative name(s):
    JmjC domain-containing histone demethylation protein 1D
    Lysine-specific demethylase 7
    Gene namesi
    Name:KDM7A
    Synonyms:JHDM1D, KDM7, KIAA1718
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 7

    Organism-specific databases

    HGNCiHGNC:22224. KDM7A.

    Subcellular locationi

    GO - Cellular componenti

    • nucleolus Source: HPA
    • nucleoplasm Source: HPA
    • nucleus Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi282H → A: Abolishes enzymatic activity. 1 Publication1

    Organism-specific databases

    OpenTargetsiENSG00000006459.
    PharmGKBiPA162392512.

    Chemistry databases

    ChEMBLiCHEMBL2163177.
    GuidetoPHARMACOLOGYi2686.

    Polymorphism and mutation databases

    BioMutaiJHDM1D.
    DMDMi90111764.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002267711 – 941Lysine-specific demethylase 7AAdd BLAST941

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei604PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiQ6ZMT4.
    PaxDbiQ6ZMT4.
    PeptideAtlasiQ6ZMT4.
    PRIDEiQ6ZMT4.

    PTM databases

    iPTMnetiQ6ZMT4.
    PhosphoSitePlusiQ6ZMT4.

    Expressioni

    Gene expression databases

    BgeeiENSG00000006459.
    CleanExiHS_JHDM1D.
    ExpressionAtlasiQ6ZMT4. baseline and differential.
    GenevisibleiQ6ZMT4. HS.

    Organism-specific databases

    HPAiHPA012114.

    Interactioni

    GO - Molecular functioni

    • methylated histone binding Source: UniProtKB

    Protein-protein interaction databases

    IntActiQ6ZMT4. 1 interactor.
    STRINGi9606.ENSP00000380692.

    Chemistry databases

    BindingDBiQ6ZMT4.

    Structurei

    Secondary structure

    1941
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni40 – 43Combined sources4
    Beta strandi52 – 55Combined sources4
    Turni56 – 58Combined sources3
    Beta strandi61 – 63Combined sources3
    Helixi64 – 67Combined sources4
    Helixi71 – 76Combined sources6
    Beta strandi77 – 80Combined sources4
    Helixi83 – 89Combined sources7
    Beta strandi100 – 104Combined sources5
    Helixi120 – 128Combined sources9
    Helixi134 – 136Combined sources3
    Turni143 – 145Combined sources3
    Helixi148 – 154Combined sources7
    Beta strandi160 – 164Combined sources5
    Turni166 – 168Combined sources3
    Helixi179 – 186Combined sources8
    Turni187 – 189Combined sources3
    Beta strandi190 – 196Combined sources7
    Turni197 – 200Combined sources4
    Beta strandi201 – 206Combined sources6
    Helixi207 – 215Combined sources9
    Beta strandi216 – 218Combined sources3
    Beta strandi223 – 229Combined sources7
    Beta strandi231 – 233Combined sources3
    Helixi234 – 238Combined sources5
    Helixi243 – 248Combined sources6
    Helixi250 – 254Combined sources5
    Beta strandi269 – 273Combined sources5
    Beta strandi278 – 282Combined sources5
    Helixi285 – 287Combined sources3
    Beta strandi289 – 304Combined sources16
    Helixi308 – 318Combined sources11
    Helixi321 – 325Combined sources5
    Helixi328 – 331Combined sources4
    Beta strandi336 – 341Combined sources6
    Beta strandi345 – 348Combined sources4
    Beta strandi353 – 369Combined sources17
    Helixi375 – 388Combined sources14
    Helixi391 – 395Combined sources5
    Helixi399 – 418Combined sources20
    Turni419 – 421Combined sources3
    Helixi426 – 442Combined sources17
    Turni445 – 447Combined sources3
    Helixi448 – 450Combined sources3
    Helixi452 – 454Combined sources3
    Beta strandi457 – 459Combined sources3
    Helixi461 – 477Combined sources17

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3KV5X-ray2.39A/D1-488[»]
    3KV6X-ray2.89A/D1-488[»]
    3KV9X-ray2.29A92-488[»]
    3KVAX-ray2.79A92-488[»]
    3KVBX-ray2.69A92-488[»]
    3U78X-ray2.69A92-488[»]
    ProteinModelPortaliQ6ZMT4.
    SMRiQ6ZMT4.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ6ZMT4.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini230 – 386JmjCPROSITE-ProRule annotationAdd BLAST157

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni97 – 114LinkerAdd BLAST18

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi2 – 31Ala-richAdd BLAST30

    Domaini

    The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2.1 Publication
    The linker region is a critical determinant of demethylase specificity. It prevents the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3, while it favors selectivity toward H3K27me2.1 Publication

    Sequence similaritiesi

    Contains 1 JmjC domain.PROSITE-ProRule annotation
    Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Zinc fingeri37 – 88PHD-typePROSITE-ProRule annotationAdd BLAST52

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiKOG1633. Eukaryota.
    ENOG410XQXU. LUCA.
    GeneTreeiENSGT00550000074396.
    HOGENOMiHOG000231232.
    HOVERGENiHBG045631.
    InParanoidiQ6ZMT4.
    KOiK11445.
    OMAiIAKKLSW.
    OrthoDBiEOG091G09DB.
    PhylomeDBiQ6ZMT4.
    TreeFamiTF106480.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q6ZMT4-1) [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

            10         20         30         40         50
    MAGAAAAVAA GAAAGAAAAA VSVAAPGRAS APPPPPPVYC VCRQPYDVNR
    60 70 80 90 100
    FMIECDICKD WFHGSCVGVE EHHAVDIDLY HCPNCAVLHG SSLMKKRRNW
    110 120 130 140 150
    HRHDYTEIDD GSKPVQAGTR TFIKELRSRV FPSADEIIIK MHGSQLTQRY
    160 170 180 190 200
    LEKHGFDVPI MVPKLDDLGL RLPSPTFSVM DVERYVGGDK VIDVIDVARQ
    210 220 230 240 250
    ADSKMTLHNY VKYFMNPNRP KVLNVISLEF SDTKMSELVE VPDIAKKLSW
    260 270 280 290 300
    VENYWPDDSV FPKPFVQKYC LMGVQDSYTD FHIDFGGTSV WYHVLWGEKI
    310 320 330 340 350
    FYLIKPTDEN LARYESWSSS VTQSEVFFGD KVDKCYKCVV KQGHTLFVPT
    360 370 380 390 400
    GWIHAVLTSQ DCMAFGGNFL HNLNIGMQLR CYEMEKRLKT PDLFKFPFFE
    410 420 430 440 450
    AICWFVAKNL LETLKELRED GFQPQTYLVQ GVKALHTALK LWMKKELVSE
    460 470 480 490 500
    HAFEIPDNVR PGHLIKELSK VIRAIEEENG KPVKSQGIPI VCPVSRSSNE
    510 520 530 540 550
    ATSPYHSRRK MRKLRDHNVR TPSNLDILEL HTREVLKRLE MCPWEEDILS
    560 570 580 590 600
    SKLNGKFNKH LQPSSTVPEW RAKDNDLRLL LTNGRIIKDE RQPFADQSLY
    610 620 630 640 650
    TADSENEEDK RRTKKAKMKI EESSGVEGVE HEESQKPLNG FFTRVKSELR
    660 670 680 690 700
    SRSSGYSDIS ESEDSGPECT ALKSIFTTEE SESSGDEKKQ EITSNFKEES
    710 720 730 740 750
    NVMRNFLQKS QKPSRSEIPI KRECPTSTST EEEAIQGMLS MAGLHYSTCL
    760 770 780 790 800
    QRQIQSTDCS GERNSLQDPS SCHGSNHEVR QLYRYDKPVE CGYHVKTEDP
    810 820 830 840 850
    DLRTSSWIKQ FDTSRFHPQD LSRSQKCIRK EGSSEISQRV QSRNYVDSSG
    860 870 880 890 900
    SSLQNGKYMQ NSNLTSGACQ ISNGSLSPER PVGETSFSVP LHPTKRPASN
    910 920 930 940
    PPPISNQATK GKRPKKGMAT AKQRLGKILK LNRNGHARFF V
    Length:941
    Mass (Da):106,557
    Last modified:March 7, 2006 - v2
    Checksum:iAB8161020D157F11
    GO
    Isoform 2 (identifier: Q6ZMT4-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         792-809: GYHVKTEDPDLRTSSWIK → ETRSHLCCPDWSPTPELK
         810-941: Missing.

    Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available.
    Show »
    Length:809
    Mass (Da):92,001
    Checksum:i1561533C92AB3466
    GO

    Sequence cautioni

    The sequence BAD18641 differs from that shown. Reason: Frameshift at position 902.Curated
    The sequence EAL24032 differs from that shown. Reason: Erroneous gene model prediction.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti677T → I in CAE46011 (PubMed:17974005).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_049652392D → Y.Corresponds to variant rs5020212dbSNPEnsembl.1
    Natural variantiVAR_049653644R → S.1 PublicationCorresponds to variant rs6950119dbSNPEnsembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_017458792 – 809GYHVK…SSWIK → ETRSHLCCPDWSPTPELK in isoform 2. 1 PublicationAdd BLAST18
    Alternative sequenceiVSP_017459810 – 941Missing in isoform 2. 1 PublicationAdd BLAST132

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK131497 mRNA. Translation: BAD18641.1. Frameshift.
    AC004849 Genomic DNA. No translation available.
    CH236950 Genomic DNA. Translation: EAL24032.1. Sequence problems.
    AB051505 mRNA. Translation: BAB21809.1.
    BX641017 mRNA. Translation: CAE46011.1.
    CCDSiCCDS43658.1. [Q6ZMT4-1]
    RefSeqiNP_085150.1. NM_030647.1. [Q6ZMT4-1]
    UniGeneiHs.308710.

    Genome annotation databases

    EnsembliENST00000397560; ENSP00000380692; ENSG00000006459. [Q6ZMT4-1]
    GeneIDi80853.
    KEGGihsa:80853.
    UCSCiuc003vvm.4. human. [Q6ZMT4-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK131497 mRNA. Translation: BAD18641.1. Frameshift.
    AC004849 Genomic DNA. No translation available.
    CH236950 Genomic DNA. Translation: EAL24032.1. Sequence problems.
    AB051505 mRNA. Translation: BAB21809.1.
    BX641017 mRNA. Translation: CAE46011.1.
    CCDSiCCDS43658.1. [Q6ZMT4-1]
    RefSeqiNP_085150.1. NM_030647.1. [Q6ZMT4-1]
    UniGeneiHs.308710.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3KV5X-ray2.39A/D1-488[»]
    3KV6X-ray2.89A/D1-488[»]
    3KV9X-ray2.29A92-488[»]
    3KVAX-ray2.79A92-488[»]
    3KVBX-ray2.69A92-488[»]
    3U78X-ray2.69A92-488[»]
    ProteinModelPortaliQ6ZMT4.
    SMRiQ6ZMT4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiQ6ZMT4. 1 interactor.
    STRINGi9606.ENSP00000380692.

    Chemistry databases

    BindingDBiQ6ZMT4.
    ChEMBLiCHEMBL2163177.
    GuidetoPHARMACOLOGYi2686.

    PTM databases

    iPTMnetiQ6ZMT4.
    PhosphoSitePlusiQ6ZMT4.

    Polymorphism and mutation databases

    BioMutaiJHDM1D.
    DMDMi90111764.

    Proteomic databases

    MaxQBiQ6ZMT4.
    PaxDbiQ6ZMT4.
    PeptideAtlasiQ6ZMT4.
    PRIDEiQ6ZMT4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000397560; ENSP00000380692; ENSG00000006459. [Q6ZMT4-1]
    GeneIDi80853.
    KEGGihsa:80853.
    UCSCiuc003vvm.4. human. [Q6ZMT4-1]

    Organism-specific databases

    CTDi80853.
    GeneCardsiKDM7A.
    H-InvDBHIX0007139.
    HGNCiHGNC:22224. KDM7A.
    HPAiHPA012114.
    neXtProtiNX_Q6ZMT4.
    OpenTargetsiENSG00000006459.
    PharmGKBiPA162392512.
    HUGEiSearch...
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG1633. Eukaryota.
    ENOG410XQXU. LUCA.
    GeneTreeiENSGT00550000074396.
    HOGENOMiHOG000231232.
    HOVERGENiHBG045631.
    InParanoidiQ6ZMT4.
    KOiK11445.
    OMAiIAKKLSW.
    OrthoDBiEOG091G09DB.
    PhylomeDBiQ6ZMT4.
    TreeFamiTF106480.

    Enzyme and pathway databases

    ReactomeiR-HSA-3214842. HDMs demethylate histones.
    R-HSA-6802952. Signaling by BRAF and RAF fusions.

    Miscellaneous databases

    EvolutionaryTraceiQ6ZMT4.
    GenomeRNAii80853.
    PROiQ6ZMT4.

    Gene expression databases

    BgeeiENSG00000006459.
    CleanExiHS_JHDM1D.
    ExpressionAtlasiQ6ZMT4. baseline and differential.
    GenevisibleiQ6ZMT4. HS.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR019786. Zinc_finger_PHD-type_CS.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR019787. Znf_PHD-finger.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF02373. JmjC. 1 hit.
    PF00628. PHD. 1 hit.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    PS01359. ZF_PHD_1. 1 hit.
    PS50016. ZF_PHD_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiKDM7A_HUMAN
    AccessioniPrimary (citable) accession number: Q6ZMT4
    Secondary accession number(s): A4D1S9
    , C9JJH9, C9JQU2, Q6MZL8, Q9C0E5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 7, 2006
    Last sequence update: March 7, 2006
    Last modified: November 30, 2016
    This is version 114 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 7
      Human chromosome 7: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.