Q6B0I6 · KDM4D_HUMAN
- ProteinLysine-specific demethylase 4D
- GeneKDM4D
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids523 (go to sequence)
- Protein existenceEvidence at protein 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 | 136 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: Y | ||||||
Binding site | 192 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 194 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Binding site | 202 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 210 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 238 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 244 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 245 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 280 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 310 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 312 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | blood microparticle | |
Cellular Component | chromatin | |
Cellular Component | nucleoplasm | |
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 | double-strand break repair via homologous recombination | |
Biological Process | inflammatory response | |
Biological Process | positive regulation of chromatin binding | |
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
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ6B0I6
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Disease & Variants
Features
Showing features for natural variant.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Natural variant | VAR_057882 | 355 | in dbSNP:rs35631512 | |||
Sequence: S → R | ||||||
Natural variant | VAR_026225 | 408 | in dbSNP:rs3740853 | |||
Sequence: R → Q | ||||||
Natural variant | VAR_057883 | 471 | in dbSNP:rs34366036 | |||
Sequence: A → S |
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.
Organism-specific databases
Miscellaneous
Chemistry
Genetic variation databases
PTM/Processing
Features
Showing features for chain, modified residue, modified residue (large scale data).
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Chain | PRO_0000234376 | 1-523 | UniProt | Lysine-specific demethylase 4D | |||
Sequence: METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDRAVVDHMEPRVPASQELSTQKEVQLPRRAALGLRQLPSHWARHSPWPMAARSGTRCHTLVCSSLPRRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQIIHPSNGRRGRGRPPQKLRAQELTLQTPAKRPLLAGTTCTASGPEPEPLPEDGALMDKPVPLSPGLQHPVKASGCSWAPVP | |||||||
Modified residue | 26 | UniProt | PolyADP-ribosyl glutamic acid | ||||
Sequence: E | |||||||
Modified residue | 27 | UniProt | PolyADP-ribosyl glutamic acid | ||||
Sequence: E | |||||||
Modified residue (large scale data) | 355 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 505 | PRIDE | Phosphoserine | ||||
Sequence: S |
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
Interaction
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q6B0I6 | CEP76 Q8TAP6 | 3 | EBI-4311651, EBI-742887 |
Protein-protein interaction databases
Chemistry
Miscellaneous
Structure
Family & Domains
Features
Showing features for domain, compositional bias, region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 18-60 | JmjN | ||||
Sequence: IMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKAR | ||||||
Domain | 146-312 | JmjC | ||||
Sequence: DENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSC | ||||||
Compositional bias | 407-443 | Polar residues | ||||
Sequence: RRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQI | ||||||
Region | 407-523 | Disordered | ||||
Sequence: RRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQIIHPSNGRRGRGRPPQKLRAQELTLQTPAKRPLLAGTTCTASGPEPEPLPEDGALMDKPVPLSPGLQHPVKASGCSWAPVP |
Sequence similarities
Belongs to the JHDM3 histone demethylase family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length523
- Mass (Da)58,603
- Last updated2009-06-16 v3
- Checksum5303A0846ECEBA58
Sequence caution
Features
Showing features for compositional bias, sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 407-443 | Polar residues | ||||
Sequence: RRSAVSGTATQPRAAAVHSSKKPSSTPSSTPGPSAQI | ||||||
Sequence conflict | 510 | in Ref. 4; AAH74739 | ||||
Sequence: H → R |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |