Q5XUN4 · KDM5D_PANTR

Function

function

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).

Catalytic activity

Cofactor

Protein has several cofactor binding sites:
L-ascorbate (UniProtKB | Rhea| CHEBI:38290 )

Fe2+ (UniProtKB | Rhea| CHEBI:29033 )

Note: Binds 1 Fe2+ ion per subunit.

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site4302-oxoglutarate (UniProtKB | ChEBI)
Binding site504Fe cation (UniProtKB | ChEBI); catalytic
Binding site506Fe cation (UniProtKB | ChEBI); catalytic
Binding site5122-oxoglutarate (UniProtKB | ChEBI)
Binding site5142-oxoglutarate (UniProtKB | ChEBI)
Binding site5222-oxoglutarate (UniProtKB | ChEBI)
Binding site592Fe cation (UniProtKB | ChEBI); catalytic

GO annotations

AspectTerm
Cellular Componentchromatin
Cellular Componentnucleus
Molecular FunctionDNA binding
Molecular Functionhistone H3K4me/H3K4me2/H3K4me3 demethylase activity
Molecular Functionmetal ion binding
Biological Processchromatin remodeling
Biological Processregulation of DNA-templated transcription

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Lysine-specific demethylase 5D
  • EC number
  • Alternative names
    • Histone demethylase JARID1D
    • Jumonji/ARID domain-containing protein 1D
    • Protein SmcY
    • [histone H3]-trimethyl-L-lysine(4) demethylase 5D

Gene names

    • Name
      KDM5D
    • Synonyms
      JARID1D, SMCY

Organism names

  • Taxonomic identifier
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Pan

Accessions

  • Primary accession
    Q5XUN4

Proteomes

Subcellular Location

Nucleus

Keywords

PTM/Processing

Features

Showing features for chain, cross-link, modified residue.

TypeIDPosition(s)Description
ChainPRO_00002005901-1535Lysine-specific demethylase 5D
Cross-link205Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross-link229Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross-link244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross-link272Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Modified residue291Phosphoserine
Modified residue307Phosphoserine
Modified residue884Phosphoserine
Modified residue1342Phosphoserine

Keywords

Proteomic databases

Interaction

Subunit

Interacts withPCGF6, MSH5, ZMYND8, AR.

Protein-protein interaction databases

Family & Domains

Features

Showing features for domain, region, compositional bias, zinc finger.

TypeIDPosition(s)Description
Domain14-55JmjN
Domain79-169ARID
Region192-227Disordered
Compositional bias197-211Polar residues
Compositional bias212-227Basic and acidic residues
Zinc finger314-364PHD-type 1
Domain458-624JmjC
Zinc finger697-749C5HC2
Zinc finger1174-1235PHD-type 2
Region1425-1519Disordered
Compositional bias1447-1467Polar residues
Compositional bias1474-1489Basic and acidic residues
Compositional bias1490-1519Polar residues

Domain

The JmjC domain is required for enzymatic activity.

Sequence similarities

Belongs to the JARID1 histone demethylase family.

Keywords

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    1,535
  • Mass (Da)
    173,743
  • Last updated
    2004-11-23 v1
  • Checksum
    D1C6E59F8A02C435
MEPGCNEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNFRFTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGANHVQCNTHPFDNEVKDKEYKPHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEEDIEKNPELKKLQIYGPGPKMMGLGLMAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTMQLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAECKQPPEAFGFEQATQEYTLQSFGEMADSFKSDYFNMPVHMVPTELLEKEFWRLVSSIEEDVTVEYGADIHYKEFGSGFPVSNSKQNLSPEEKEYATSGWNLNVMPVLAQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKMLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDLNLAVAVHKEMFIMVQEERRLRKALLEKGVTEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPTMLHKLKIRAESFDTWANKVRVALEVEDGRKRSFEELRALESEARERRFPNSELLQRLKNCLSEVEACIAQVLGLVSGQVARMDTPQLTLTELRVLLEQMGSLPCAMHQIGDVKDVLEQVEAYQDEAREALATLPSSPGLLRSLLERGQQLGVEVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASSPSVDKARAELQELLTIAERWEEKAHFCLEARQKHPPATLEAIIRETENIPVHLPNIQALKEALTKAQAWIADVDEIQNGDHYPCLDDLEGLVAVGRDLPVGLEELRQLELQVLTAHSWREKASKTFLKKNSCYTLLEVLCPCADAGSDSTKRSRWMEKALGLYQCDTELLGLSAQDLRDPGSLIVAFKEGEQKEKEGILQLRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGALQCDLCQDWFHGQCVSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLVALQRLPVRLPEGEALQCLTERAIGWQDRARKALASEDVTALLRHLAELRQQLQAKPRPVYTSATACDPIREGSGNNISKVQGLLENGDSVISPENMAPGKGSDLELLSSLLPQLTGPVLELPEAIRAPLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLDRIRTLLELEKFEHQGSRTRSRALERRRRQQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDHSPSLKGNQNSLQHKDSGSSAACPSLMPWLQLSYSDEQQL

Features

Showing features for compositional bias.

TypeIDPosition(s)Description
Compositional bias197-211Polar residues
Compositional bias212-227Basic and acidic residues
Compositional bias1447-1467Polar residues
Compositional bias1474-1489Basic and acidic residues
Compositional bias1490-1519Polar residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AY736376
EMBL· GenBank· DDBJ
AAU82116.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

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