Q3U2K5
PR
Gene name |
Kdm4d (Jhdm3d, Jmjd2d) |
Protein name |
Lysine-specific demethylase 4D |
Names |
JmjC domain-containing histone demethylation protein 3D, Jumonji domain-containing protein 2D, [histone H3]-trimethyl-L-lysine(9) demethylase 4D |
Species |
Mus musculus (Mouse) |
KEGG Pathway |
mmu:244694 |
EC number |
1.14.11.66: With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors |
Protein Class |
|
Descriptions
The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.
Autoinhibitory domains (AIDs)
Target domain |
|
Relief mechanism |
|
Assay |
cis-regPred |
Accessory elements
No accessory elements
Autoinhibited structure
Activated structure
1 structures for Q3U2K5
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| AF-Q3U2K5-F1 | Predicted | AlphaFoldDB |
28 variants for Q3U2K5
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
| rs3389022473 | 12 | N>I | No | EVA | |
| rs3388999473 | 20 | P>R | No | EVA | |
| rs3389030739 | 28 | F>I | No | EVA | |
| rs3389024599 | 46 | A>V | No | EVA | |
| rs3389018771 | 67 | L>I | No | EVA | |
| rs3389030738 | 76 | V>S | No | EVA | |
| rs3389022122 | 78 | G>E | No | EVA | |
| rs50376670 | 103 | N>D | No | EVA | |
| rs3389022527 | 119 | E>K | No | EVA | |
| rs3389022512 | 129 | E>V | No | EVA | |
| rs3388999399 | 140 | S>T | No | EVA | |
| rs3389027220 | 186 | F>C | No | EVA | |
| rs3389027210 | 202 | H>Y | No | EVA | |
| rs3389024658 | 267 | E>D | No | EVA | |
| rs3388999393 | 323 | R>T | No | EVA | |
| rs3389029868 | 345 | T>S | No | EVA | |
| rs3389022509 | 349 | V>L | No | EVA | |
| rs48286567 | 351 | T>S | No | EVA | |
| rs250328080 | 376 | R>C | No | EVA | |
| rs3389018820 | 387 | T>M | No | EVA | |
| rs3389017602 | 438 | C>S | No | EVA | |
| rs224848271 | 439 | S>G | No | EVA | |
| rs3389022131 | 446 | E>G | No | EVA | |
| rs3399813852 | 468 | D>E | No | EVA | |
| rs3399830714 | 469 | T>R | No | EVA | |
| rs260045842 | 474 | E>G | No | EVA | |
| rs242835731 | 487 | D>N | No | EVA | |
| rs211740180 | 495 | P>L | No | EVA |
No associated diseases with Q3U2K5
Functions
| Description | ||
|---|---|---|
| EC Number | 1.14.11.66 | With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors |
| Subcellular Localization |
|
|
| PANTHER Family | ||
| PANTHER Subfamily | ||
| PANTHER Protein Class | ||
| PANTHER Pathway Category | No pathway information available | |
3 GO annotations of cellular component
| Name | Definition |
|---|---|
| nucleus | A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. |
| pericentric heterochromatin | Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3). |
| site of double-strand break | A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix. |
6 GO annotations of molecular function
| Name | Definition |
|---|---|
| chromatin DNA binding | Binding to DNA that is assembled into chromatin. |
| damaged DNA binding | Binding to damaged DNA. |
| histone demethylase activity | Catalysis of the removal of a methyl group from a histone. |
| histone H3-methyl-lysine-9 demethylase activity | Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein. |
| histone H3-tri/dimethyl-lysine-9 demethylase activity | Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. |
| metal ion binding | Binding to a metal ion. |
9 GO annotations of biological process
| Name | Definition |
|---|---|
| cellular response to DNA damage stimulus | Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. |
| cellular response to ionizing radiation | Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays. |
| chromatin remodeling | A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. |
| double-strand break repair via homologous recombination | The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule. |
| histone H3-K9 demethylation | The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. |
| negative regulation of histone H3-K9 trimethylation | Any process that stops, prevents or reduces the frequency, rate or extent of histone H3-K9 trimethylation. |
| positive regulation of chromatin binding | Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase. |
| positive regulation of double-strand break repair via nonhomologous end joining | Any process that activates or increases the frequency, rate or extent of double-strand break repair via nonhomologous end joining. |
| regulation of protein phosphorylation | Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein. |
4 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| O94953 | KDM4B | Lysine-specific demethylase 4B | Homo sapiens (Human) | PR |
| O75164 | KDM4A | Lysine-specific demethylase 4A | Homo sapiens (Human) | PR |
| Q62240 | Kdm5d | Lysine-specific demethylase 5D | Mus musculus (Mouse) | PR |
| Q8BW72 | Kdm4a | Lysine-specific demethylase 4A | Mus musculus (Mouse) | PR |
| 10 | 20 | 30 | 40 | 50 | 60 |
| MKTKSTCAQN | PNCSIMIFRP | TKEEFNDFDK | YIAYMESQGA | HRAGLAKVIP | PKEWRARQSY |
| 70 | 80 | 90 | 100 | 110 | 120 |
| DNISNILIAT | PLQQVVSGQA | GVFTQYHKKK | KGMTVGEYRE | LANSKKYQTP | PHLDFEDLER |
| 130 | 140 | 150 | 160 | 170 | 180 |
| KYWKNRLYES | PIYGADVSGS | LFDGKTQQWN | VGHLGTIQDL | LEQECGIVIE | GVNTPYLYFG |
| 190 | 200 | 210 | 220 | 230 | 240 |
| MWKTTFAWHT | EDMDLYSINY | LHFGQPKTWY | AVPPEHGRRL | ERLARELFPG | SSQGCQAFLR |
| 250 | 260 | 270 | 280 | 290 | 300 |
| HKVALISPTV | LKENGIPFGR | ITQEAGEFMV | TFPYGYHAGF | NHGFNCAEAI | NFATPRWIDY |
| 310 | 320 | 330 | 340 | 350 | 360 |
| GKVASQCSCG | EARVSFSMDA | FVRILQPERY | ELWKRGQDQA | VVDHTETMVS | TSQELTTRRV |
| 370 | 380 | 390 | 400 | 410 | 420 |
| TKAPRKTWGL | KRLRLRQVSR | SLLPIATVSN | VPCNMQVCHT | SRQPSDVKGD | DVQKSDSARA |
| 430 | 440 | 450 | 460 | 470 | 480 |
| SPHPLSLPSS | GHMSTRRCSL | GRRPCELGAQ | ESSNGAPVKR | QLPAGRDDTS | PSPELQPQAV |
| 490 | 500 | ||||
| SGDLIVDSGL | VNPGPQHLMT | ASEGGLTSDP |