Q3U2K5 · KDM4D_MOUSE

  • Protein
    Lysine-specific demethylase 4D
  • Gene
    Kdm4d
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at transcript 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.

Catalytic activity

Cofactor

Fe2+ (UniProtKB | Rhea| CHEBI:29033 )

Note: Binds 1 Fe2+ ion per subunit.

Features

Showing features for binding site.

151050100150200250300350400450500
TypeIDPosition(s)Description
Binding site1332-oxoglutarate (UniProtKB | ChEBI)
Binding site189Fe cation (UniProtKB | ChEBI); catalytic
Binding site191Fe cation (UniProtKB | ChEBI); catalytic
Binding site1992-oxoglutarate (UniProtKB | ChEBI)
Binding site2072-oxoglutarate (UniProtKB | ChEBI)
Binding site235Zn2+ (UniProtKB | ChEBI)
Binding site241Zn2+ (UniProtKB | ChEBI)
Binding site2422-oxoglutarate (UniProtKB | ChEBI)
Binding site277Fe cation (UniProtKB | ChEBI); catalytic
Binding site307Zn2+ (UniProtKB | ChEBI)
Binding site309Zn2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentchromatin
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 ProcessDNA damage response
Biological Processdouble-strand break repair via homologous recombination
Biological Processinflammatory response
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
  • Strains
    • C57BL/6J
    • NOD
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus

Accessions

  • Primary accession
    Q3U2K5
  • Secondary accessions
    • A2CGB5
    • B8JK34
    • Q2M1G7
    • Q8BI19

Proteomes

Organism-specific databases

Subcellular Location

Keywords

PTM/Processing

Features

Showing features for chain, modified residue.

TypeIDPosition(s)Description
ChainPRO_00002343771-510Lysine-specific demethylase 4D
Modified residue23PolyADP-ribosyl glutamic acid
Modified residue24PolyADP-ribosyl glutamic acid

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

Interaction

Protein-protein interaction databases

Miscellaneous

Structure

Family & Domains

Features

Showing features for domain, region, compositional bias.

TypeIDPosition(s)Description
Domain15-57JmjN
Domain143-309JmjC
Region397-510Disordered
Compositional bias419-436Polar residues

Sequence similarities

Belongs to the JHDM3 histone demethylase family.

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    510
  • Mass (Da)
    57,212
  • Last updated
    2006-05-16 v2
  • Checksum
    6B57A0300BAD94C9
MKTKSTCAQNPNCSIMIFRPTKEEFNDFDKYIAYMESQGAHRAGLAKVIPPKEWRARQSYDNISNILIATPLQQVVSGQAGVFTQYHKKKKGMTVGEYRELANSKKYQTPPHLDFEDLERKYWKNRLYESPIYGADVSGSLFDGKTQQWNVGHLGTIQDLLEQECGIVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGQPKTWYAVPPEHGRRLERLARELFPGSSQGCQAFLRHKVALISPTVLKENGIPFGRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKVASQCSCGEARVSFSMDAFVRILQPERYELWKRGQDQAVVDHTETMVSTSQELTTRRVTKAPRKTWGLKRLRLRQVSRSLLPIATVSNVPCNMQVCHTSRQPSDVKGDDVQKSDSARASPHPLSLPSSGHMSTRRCSLGRRPCELGAQESSNGAPVKRQLPAGRDDTSPSPELQPQAVSGDLIVDSGLVNPGPQHLMTASEGGLTSDP

Computationally mapped potential isoform sequences

There is 1 potential isoform mapped to this entry

View all
EntryEntry nameGene nameLength
Z4YLE9Z4YLE9_MOUSEKdm4d450

Sequence caution

The sequence BAC26740.1 differs from that shown. Reason: Erroneous initiation Truncated N-terminus.
The sequence BAC26740.1 differs from that shown. Reason: Erroneous termination Truncated C-terminus.
The sequence BAE33135.1 differs from that shown. Reason: Frameshift

Features

Showing features for sequence conflict, compositional bias.

TypeIDPosition(s)Description
Sequence conflict374in Ref. 1; BAC26740
Compositional bias419-436Polar residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AK030020
EMBL· GenBank· DDBJ
BAC26740.1
EMBL· GenBank· DDBJ
mRNA Sequence problems.
AK155227
EMBL· GenBank· DDBJ
BAE33135.1
EMBL· GenBank· DDBJ
mRNA Frameshift
CT485607
EMBL· GenBank· DDBJ
-Genomic DNA No translation available.
BC112372
EMBL· GenBank· DDBJ
AAI12373.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

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