O94953
Gene name |
KDM4B (JHDM3B, JMJD2B, KIAA0876) |
Protein name |
Lysine-specific demethylase 4B |
Names |
JmjC domain-containing histone demethylation protein 3B, Jumonji domain-containing protein 2B, [histone H3]-trimethyl-L-lysine(9) demethylase 4B |
Species |
Homo sapiens (Human) |
KEGG Pathway |
hsa:23030 |
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
4 structures for O94953
| Entry ID | Method | Resolution | Chain | Position | Source |
|---|---|---|---|---|---|
| 4LXL | X-ray | 187 A | A | 1-348 | PDB |
| 4UC4 | X-ray | 256 A | A/B | 917-1031 | PDB |
| 7JM5 | X-ray | 270 A | A/B | 1-366 | PDB |
| AF-O94953-F1 | Predicted | AlphaFoldDB |
6 variants for O94953
| Variant ID(s) | Position | Change | Description | Diseaes Association | Provenance |
|---|---|---|---|---|---|
| VAR_085967 | 220 | L>P | MRD65 [UniProt] | Yes | UniProt |
| VAR_085968 | 222 | R>W | MRD65 [UniProt] | Yes | UniProt |
| VAR_085969 | 768 | H>R | MRD65 [UniProt] | Yes | UniProt |
| VAR_085970 | 1095 | P>L | MRD65; unknown pathological significance [UniProt] | Yes | UniProt |
|
rs11667206 VAR_026223 |
29 | N>T | No |
UniProt dbSNP |
|
|
VAR_026224 rs2620836 |
710 | K>E | No |
UniProt dbSNP |
1 associated diseases with O94953
[MIM: 619320]: Intellectual developmental disorder, autosomal dominant 65 (MRD65)
An autosomal dominant form of intellectual disability, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD65 is characterized by delayed motor and speech acquisition, variably impaired intellectual development, behavioral abnormalities, and dysmorphic facial features. Additional variable features include feeding difficulties, hypotonia, and seizures. {ECO:0000269|PubMed:33232677}. Note=The disease is caused by variants affecting the gene represented in this entry.
Without disease ID
- An autosomal dominant form of intellectual disability, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD65 is characterized by delayed motor and speech acquisition, variably impaired intellectual development, behavioral abnormalities, and dysmorphic facial features. Additional variable features include feeding difficulties, hypotonia, and seizures. {ECO:0000269|PubMed:33232677}. Note=The disease is caused by variants affecting the gene represented in this entry.
10 regional properties for O94953
| Type | Name | Position | InterPro Accession |
|---|---|---|---|
| domain | Zinc finger, PHD-type | 731 - 789 | IPR001965-1 |
| domain | Zinc finger, PHD-type | 851 - 907 | IPR001965-2 |
| domain | Tudor domain | 917 - 974 | IPR002999-1 |
| domain | Tudor domain | 975 - 1031 | IPR002999-2 |
| domain | JmjC domain | 143 - 309 | IPR003347 |
| domain | JmjN domain | 14 - 57 | IPR003349 |
| domain | Extended PHD (ePHD) domain | 794 - 907 | IPR034732 |
| domain | Lysine-specific demethylase 4-like, Tudor domain | 922 - 956 | IPR040477-1 |
| domain | Lysine-specific demethylase 4-like, Tudor domain | 980 - 1014 | IPR040477-2 |
| domain | Lysine-specific demethylase 4B, first Tudor domain | 919 - 972 | IPR047483 |
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 | |
2 GO annotations of cellular component
| Name | Definition |
|---|---|
| nucleoplasm | That part of the nuclear content other than the chromosomes or the nucleolus. |
| 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. |
5 GO annotations of molecular function
| Name | Definition |
|---|---|
| histone demethylase activity | Catalysis of the removal of a methyl group from a histone. |
| histone H3-methyl-lysine-36 demethylase activity | Catalysis of the removal of a methyl group from a modified lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate. |
| 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. |
4 GO annotations of biological process
| Name | Definition |
|---|---|
| brain development | The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.). |
| 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. |
| histone H3-K36 demethylation | The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone. |
| histone H3-K9 demethylation | The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone. |
4 homologous proteins in AiPD
| UniProt AC | Gene Name | Protein Name | Species | Evidence Code |
|---|---|---|---|---|
| Q9BY66 | KDM5D | Lysine-specific demethylase 5D | Homo sapiens (Human) | PR |
| O75164 | KDM4A | Lysine-specific demethylase 4A | Homo sapiens (Human) | PR |
| Q3U2K5 | Kdm4d | Lysine-specific demethylase 4D | Mus musculus (Mouse) | PR |
| Q8BW72 | Kdm4a | Lysine-specific demethylase 4A | Mus musculus (Mouse) | PR |
| 10 | 20 | 30 | 40 | 50 | 60 |
| MGSEDHGAQN | PSCKIMTFRP | TMEEFKDFNK | YVAYIESQGA | HRAGLAKIIP | PKEWKPRQTY |
| 70 | 80 | 90 | 100 | 110 | 120 |
| DDIDDVVIPA | PIQQVVTGQS | GLFTQYNIQK | KAMTVGEYRR | LANSEKYCTP | RHQDFDDLER |
| 130 | 140 | 150 | 160 | 170 | 180 |
| KYWKNLTFVS | PIYGADISGS | LYDDDVAQWN | IGSLRTILDM | VERECGTIIE | GVNTPYLYFG |
| 190 | 200 | 210 | 220 | 230 | 240 |
| MWKTTFAWHT | EDMDLYSINY | LHFGEPKSWY | AIPPEHGKRL | ERLAIGFFPG | SSQGCDAFLR |
| 250 | 260 | 270 | 280 | 290 | 300 |
| HKMTLISPII | LKKYGIPFSR | ITQEAGEFMI | TFPYGYHAGF | NHGFNCAEST | NFATLRWIDY |
| 310 | 320 | 330 | 340 | 350 | 360 |
| GKVATQCTCR | KDMVKISMDV | FVRILQPERY | ELWKQGKDLT | VLDHTRPTAL | TSPELSSWSA |
| 370 | 380 | 390 | 400 | 410 | 420 |
| SRASLKAKLL | RRSHRKRSQP | KKPKPEDPKF | PGEGTAGAAL | LEEAGGSVKE | EAGPEVDPEE |
| 430 | 440 | 450 | 460 | 470 | 480 |
| EEEEPQPLPH | GREAEGAEED | GRGKLRPTKA | KSERKKKSFG | LLPPQLPPPP | AHFPSEEALW |
| 490 | 500 | 510 | 520 | 530 | 540 |
| LPSPLEPPVL | GPGPAAMEES | PLPAPLNVVP | PEVPSEELEA | KPRPIIPMLY | VVPRPGKAAF |
| 550 | 560 | 570 | 580 | 590 | 600 |
| NQEHVSCQQA | FEHFAQKGPT | WKEPVSPMEL | TGPEDGAASS | GAGRMETKAR | AGEGQAPSTF |
| 610 | 620 | 630 | 640 | 650 | 660 |
| SKLKMEIKKS | RRHPLGRPPT | RSPLSVVKQE | ASSDEEASPF | SGEEDVSDPD | ALRPLLSLQW |
| 670 | 680 | 690 | 700 | 710 | 720 |
| KNRAASFQAE | RKFNAAAART | EPYCAICTLF | YPYCQALQTE | KEAPIASLGK | GCPATLPSKS |
| 730 | 740 | 750 | 760 | 770 | 780 |
| RQKTRPLIPE | MCFTSGGENT | EPLPANSYIG | DDGTSPLIAC | GKCCLQVHAS | CYGIRPELVN |
| 790 | 800 | 810 | 820 | 830 | 840 |
| EGWTCSRCAA | HAWTAECCLC | NLRGGALQMT | TDRRWIHVIC | AIAVPEARFL | NVIERHPVDI |
| 850 | 860 | 870 | 880 | 890 | 900 |
| SAIPEQRWKL | KCVYCRKRMK | KVSGACIQCS | YEHCSTSFHV | TCAHAAGVLM | EPDDWPYVVS |
| 910 | 920 | 930 | 940 | 950 | 960 |
| ITCLKHKSGG | HAVQLLRAVS | LGQVVITKNR | NGLYYRCRVI | GAASQTCYEV | NFDDGSYSDN |
| 970 | 980 | 990 | 1000 | 1010 | 1020 |
| LYPESITSRD | CVQLGPPSEG | ELVELRWTDG | NLYKAKFISS | VTSHIYQVEF | EDGSQLTVKR |
| 1030 | 1040 | 1050 | 1060 | 1070 | 1080 |
| GDIFTLEEEL | PKRVRSRLSL | STGAPQEPAF | SGEEAKAAKR | PRVGTPLATE | DSGRSQDYVA |
| 1090 | |||||
| FVESLLQVQG | RPGAPF |