Q3U2K5 · KDM4D_MOUSE
- ProteinLysine-specific demethylase 4D
- GeneKdm4d
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids510 (go to sequence)
- Protein existenceEvidence at transcript level
- Annotation score5/5
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
- 2 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N6-methyl-L-lysyl9-[histone H3] + 2 succinate
2 CHEBI:16810 + RHEA-COMP:15538 CHEBI:61961 Position: 9+ 2 CHEBI:15379 = 2 CHEBI:16526 + 2 CHEBI:16842 + RHEA-COMP:15542 CHEBI:61929 Position: 9+ 2 CHEBI:30031
Cofactor
Note: Binds 1 Fe2+ ion per subunit.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 133 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: Y | ||||||
Binding site | 189 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 191 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Binding site | 199 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 207 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 235 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 241 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 242 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 277 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 307 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 309 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromatin | |
Cellular Component | nucleus | |
Cellular Component | pericentric heterochromatin | |
Cellular Component | site of double-strand break | |
Molecular Function | chromatin DNA binding | |
Molecular Function | damaged DNA binding | |
Molecular Function | histone demethylase activity | |
Molecular Function | histone H3K9 demethylase activity | |
Molecular Function | histone H3K9me2/H3K9me3 demethylase activity | |
Molecular Function | metal ion binding | |
Biological Process | cellular response to ionizing radiation | |
Biological Process | chromatin remodeling | |
Biological Process | DNA damage response | |
Biological Process | double-strand break repair via homologous recombination | |
Biological Process | inflammatory response | |
Biological Process | positive regulation of double-strand break repair via nonhomologous end joining | |
Biological Process | regulation of gene expression | |
Biological Process | regulation of protein phosphorylation |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLysine-specific demethylase 4D
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus
Accessions
- Primary accessionQ3U2K5
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000234377 | 1-510 | Lysine-specific demethylase 4D | |||
Sequence: MKTKSTCAQNPNCSIMIFRPTKEEFNDFDKYIAYMESQGAHRAGLAKVIPPKEWRARQSYDNISNILIATPLQQVVSGQAGVFTQYHKKKKGMTVGEYRELANSKKYQTPPHLDFEDLERKYWKNRLYESPIYGADVSGSLFDGKTQQWNVGHLGTIQDLLEQECGIVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGQPKTWYAVPPEHGRRLERLARELFPGSSQGCQAFLRHKVALISPTVLKENGIPFGRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKVASQCSCGEARVSFSMDAFVRILQPERYELWKRGQDQAVVDHTETMVSTSQELTTRRVTKAPRKTWGLKRLRLRQVSRSLLPIATVSNVPCNMQVCHTSRQPSDVKGDDVQKSDSARASPHPLSLPSSGHMSTRRCSLGRRPCELGAQESSNGAPVKRQLPAGRDDTSPSPELQPQAVSGDLIVDSGLVNPGPQHLMTASEGGLTSDP | ||||||
Modified residue | 23 | PolyADP-ribosyl glutamic acid | ||||
Sequence: E | ||||||
Modified residue | 24 | PolyADP-ribosyl glutamic acid | ||||
Sequence: E |
Post-translational modification
Ubiquitinated via 'Lys-63'-linked ubiquitin chains. Deubiquitinated by USP14 with the help of TRIM14 leading to stabilization.
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Gene expression databases
Structure
Family & Domains
Features
Showing features for domain, region, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 15-57 | JmjN | ||||
Sequence: IMIFRPTKEEFNDFDKYIAYMESQGAHRAGLAKVIPPKEWRAR | ||||||
Domain | 143-309 | JmjC | ||||
Sequence: DGKTQQWNVGHLGTIQDLLEQECGIVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGQPKTWYAVPPEHGRRLERLARELFPGSSQGCQAFLRHKVALISPTVLKENGIPFGRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKVASQCSC | ||||||
Region | 397-510 | Disordered | ||||
Sequence: VCHTSRQPSDVKGDDVQKSDSARASPHPLSLPSSGHMSTRRCSLGRRPCELGAQESSNGAPVKRQLPAGRDDTSPSPELQPQAVSGDLIVDSGLVNPGPQHLMTASEGGLTSDP | ||||||
Compositional bias | 419-436 | Polar residues | ||||
Sequence: RASPHPLSLPSSGHMSTR |
Sequence similarities
Belongs to the JHDM3 histone demethylase family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length510
- Mass (Da)57,212
- Last updated2006-05-16 v2
- Checksum6B57A0300BAD94C9
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
Z4YLE9 | Z4YLE9_MOUSE | Kdm4d | 450 |
Sequence caution
Features
Showing features for sequence conflict, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 374 | in Ref. 1; BAC26740 | ||||
Sequence: R → L | ||||||
Compositional bias | 419-436 | Polar residues | ||||
Sequence: RASPHPLSLPSSGHMSTR |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |