Q6B0I6 · KDM4D_HUMAN

  • Protein
    Lysine-specific demethylase 4D
  • Gene
    KDM4D
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.

Caution

It is uncertain whether Met-1 or Met-4 is the initiator.

Catalytic activity

Cofactor

Fe2+ (UniProtKB | Rhea| CHEBI:29033 )

Note: Binds 1 Fe2+ ion per subunit.

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site1362-oxoglutarate (UniProtKB | ChEBI)
Binding site192Fe cation (UniProtKB | ChEBI); catalytic
Binding site194Fe cation (UniProtKB | ChEBI); catalytic
Binding site2022-oxoglutarate (UniProtKB | ChEBI)
Binding site2102-oxoglutarate (UniProtKB | ChEBI)
Binding site238Zn2+ (UniProtKB | ChEBI)
Binding site244Zn2+ (UniProtKB | ChEBI)
Binding site2452-oxoglutarate (UniProtKB | ChEBI)
Binding site280Fe cation (UniProtKB | ChEBI); catalytic
Binding site310Zn2+ (UniProtKB | ChEBI)
Binding site312Zn2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentblood microparticle
Cellular Componentchromatin
Cellular Componentnucleoplasm
Cellular Componentnucleus
Cellular Componentpericentric heterochromatin
Cellular Componentsite of double-strand break
Molecular Functionchromatin DNA binding
Molecular Functiondamaged DNA binding
Molecular Functionhistone demethylase activity
Molecular Functionhistone H3K9 demethylase activity
Molecular Functionhistone H3K9me2/H3K9me3 demethylase activity
Molecular Functionmetal ion binding
Biological Processcellular response to ionizing radiation
Biological Processchromatin remodeling
Biological Processdouble-strand break repair via homologous recombination
Biological Processinflammatory response
Biological Processpositive regulation of chromatin binding
Biological Processpositive regulation of double-strand break repair via nonhomologous end joining
Biological Processregulation of gene expression
Biological Processregulation of protein phosphorylation

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Lysine-specific demethylase 4D
  • EC number
  • Alternative names
    • JmjC domain-containing histone demethylation protein 3D
    • Jumonji domain-containing protein 2D
    • [histone H3]-trimethyl-L-lysine(9) demethylase 4D

Gene names

    • Name
      KDM4D
    • Synonyms
      JHDM3D, JMJD2D

Organism names

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

Accessions

  • Primary accession
    Q6B0I6
  • Secondary accessions
    • B3KPC4
    • Q0VF39
    • Q9NT41
    • Q9NW76

Proteomes

Organism-specific databases

Subcellular Location

Disease & Variants

Features

Showing features for natural variant.

TypeIDPosition(s)Description
Natural variantVAR_057882355in dbSNP:rs35631512
Natural variantVAR_026225408in dbSNP:rs3740853
Natural variantVAR_057883471in dbSNP:rs34366036

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 603 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

Organism-specific databases

Miscellaneous

Chemistry

Genetic variation databases

PTM/Processing

Features

Showing features for chain, modified residue, modified residue (large scale data).

TypeIDPosition(s)SourceDescription
ChainPRO_00002343761-523UniProtLysine-specific demethylase 4D
Modified residue26UniProtPolyADP-ribosyl glutamic acid
Modified residue27UniProtPolyADP-ribosyl glutamic acid
Modified residue (large scale data)355PRIDEPhosphoserine
Modified residue (large scale data)505PRIDEPhosphoserine

Post-translational modification

Ubiquitinated via 'Lys-63'-linked ubiquitin chains. Deubiquitinated by USP14 with the help of TRIM14 leading to stabilization.

Keywords

Proteomic databases

PTM databases

Expression

Gene expression databases

Organism-specific databases

Interaction

Binary interactions

TypeEntry 1Entry 2Number of experimentsIntact
BINARY Q6B0I6CEP76 Q8TAP63EBI-4311651, EBI-742887

Protein-protein interaction databases

Chemistry

Miscellaneous

Family & Domains

Features

Showing features for domain, compositional bias, region.

TypeIDPosition(s)Description
Domain18-60JmjN
Domain146-312JmjC
Compositional bias407-443Polar residues
Region407-523Disordered

Sequence similarities

Belongs to the JHDM3 histone demethylase family.

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    523
  • Mass (Da)
    58,603
  • Last updated
    2009-06-16 v3
  • Checksum
    5303A0846ECEBA58
METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDRAVVDHMEPRVPASQELSTQKEVQLPRRAALGLRQLPSHWARHSPWPMAARSGTRCHTLVCSSLPRRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQIIHPSNGRRGRGRPPQKLRAQELTLQTPAKRPLLAGTTCTASGPEPEPLPEDGALMDKPVPLSPGLQHPVKASGCSWAPVP

Sequence caution

The sequence BAA91508.1 differs from that shown. Reason: Erroneous initiation Truncated N-terminus.

Features

Showing features for compositional bias, sequence conflict.

TypeIDPosition(s)Description
Compositional bias407-443Polar residues
Sequence conflict510in Ref. 4; AAH74739

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AK001113
EMBL· GenBank· DDBJ
BAA91508.1
EMBL· GenBank· DDBJ
mRNA Different initiation
AK056162
EMBL· GenBank· DDBJ
BAG51636.1
EMBL· GenBank· DDBJ
mRNA
AP002383
EMBL· GenBank· DDBJ
-Genomic DNA No translation available.
CH471065
EMBL· GenBank· DDBJ
EAW66952.1
EMBL· GenBank· DDBJ
Genomic DNA
BC074739
EMBL· GenBank· DDBJ
AAH74739.1
EMBL· GenBank· DDBJ
mRNA
BC119010
EMBL· GenBank· DDBJ
AAI19011.1
EMBL· GenBank· DDBJ
mRNA
BC122858
EMBL· GenBank· DDBJ
AAI22859.1
EMBL· GenBank· DDBJ
mRNA
AL137545
EMBL· GenBank· DDBJ
CAB70803.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

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