P0CH95 · PHF8_DANRE
- ProteinHistone lysine demethylase PHF8
- Genephf8
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1032 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Histone lysine demethylase with selectivity for the di- and monomethyl states that plays a key role cell cycle progression, rDNA transcription and brain development. Demethylates mono- and dimethylated histone H3 'Lys-9' residue (H3K9Me1 and H3K9Me2), dimethylated H3 'Lys-27' (H3K27Me2) and monomethylated histone H4 'Lys-20' residue (H4K20Me1). Acts as a transcription activator as H3K9Me1, H3K9Me2, H3K27Me2 and H4K20Me1 are epigenetic repressive marks. Involved in cell cycle progression by being required to control G1-S transition. Acts as a coactivator of rDNA transcription, by activating polymerase I (pol I) mediated transcription of rRNA genes. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate (By similarity).
Required for brain development, probably by regulating expression of neuron-specific genes
Required for brain development, probably by regulating expression of neuron-specific genes
Catalytic activity
- 2 2-oxoglutarate + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl36-[histone H3] + 2 succinate
2 CHEBI:16810 + RHEA-COMP:9787 CHEBI:61976 Position: 36+ 2 CHEBI:15379 = 2 CHEBI:16526 + 2 CHEBI:16842 + RHEA-COMP:9785 CHEBI:29969 Position: 36+ 2 CHEBI:30031
Cofactor
Note: Binds 1 Fe2+ ion per subunit.
Features
Showing features for binding site.
GO annotations
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameHistone lysine demethylase PHF8
- EC number
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Actinopterygii > Neopterygii > Teleostei > Ostariophysi > Cypriniformes > Danionidae > Danioninae > Danio
Accessions
- Primary accessionP0CH95
Proteomes
Organism-specific databases
Subcellular Location
UniProt Annotation
GO Annotation
Note: Recruited to H3K4me3 sites on chromatin during interphase. Dissociates from chromatin when cells enter mitosis (By similarity).
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
Morpholino knockdown of the protein results in defects in brain and craniofacial development. Embryos show delays in brain development at 24 hpf and apoptosis in the developing brain and the neural tube at 30 hpf.
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 323 | Unable to rescue a phf8 morpholino mutant. | ||||
Sequence: H → Y |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000399817 | 1-1032 | Histone lysine demethylase PHF8 | |||
Sequence: MASVPVYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEDKAAEIDLYHCPNCQVTHGPSVMRKRRGAVKHADVGLGRDSGRPVKTGSAQFVRELRCRTFPSADEVLLKPTGAQLTVEFLEERSFSVPVLVLRKDGLGMNLPPSSFSVTDVEHYIGTEKEIDVIDVSRQADLKMKLGEFVEYYNSPNRDRVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEESIFERPNVQKYCLMGVKDSYTDFHIDFGGTSVWYHVLRGEKIFYLIRPTAANLSLFERWSSSSNQNELFFGDQVDMCYKCSVKQGNTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIDMQLRAYEIEKRLSTADLFKFPNFETVCWYVGKHLLDTFRGLRENRRHPATYLVHGAKALNNAFRGWTRKESLGEHEQEIPDTIKTQQLVKDLAKEIRLVEDIFQQNIGRSGTPFGGSQGLPSPHPKAQLNTPLTFSQHLSKKRGPKPKEAFGGGGVGPPGAKKKSQKGKEIKTEAGELDLLEIHTKHTLKKFQPGCKVKKSKLELPDDCLDDFEEKINKSKLKLVLTNGKLQGKKGRAGSANGAGSSLQQFQPHMATLSDFDSEDELQIDETPPPRRRPSLPSKKKLAGLPRKLPRAKPCSDPHRIREPGEVDFDIEEDYTTDEEMLTMQGVKGGAGGILDLLKASKQVAGLDSALSEEAPASPSTRDAIQGMLSMANPPSSSSSSSSSSPLSISGGGEMMGLMKEKGGREGWMSGVKKSERKAVFQRPGKRPIKRPARHLSDDESLDEQETLGTCFKDSDYVYPSLESDEEDHVSKSKMKRKRNWDDTPWSPKARVTPTLPKQERPVREGARVASVETGLAAAAAKLAQQEQQKTITKRKYTKKKTPQEKVHSTVAQLQHQPDSAPVSPPLPSEPPVDCIVEERRVEVYSASLLDHEYTAGPGPFSPGGPRGSGAMAPGVFLTSRRPSLSPQNSSSYSPSAPSPGGLVTPTSAGACQGKRPKKGLATAKQRLGKILKIHRNGKLLL |
Proteomic databases
Expression
Developmental stage
First detected at 14 hours post-fertilization (hpf) in the head and tail regions. Found mostly in the head region. Also detectable in the jaw of the embryo at 3 dpf.
Gene expression databases
Interaction
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for zinc finger, region, domain, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Zinc finger | 5-56 | PHD-type | ||||
Sequence: PVYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEDKAAEIDLYHCPNCQVT | ||||||
Region | 65-83 | Linker | ||||
Sequence: RRGAVKHADVGLGRDSGRP | ||||||
Domain | 199-355 | JmjC | ||||
Sequence: FSDTRLSNLVETPKIVRKLSWVENLWPEESIFERPNVQKYCLMGVKDSYTDFHIDFGGTSVWYHVLRGEKIFYLIRPTAANLSLFERWSSSSNQNELFFGDQVDMCYKCSVKQGNTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIDMQLRAYEIEK | ||||||
Compositional bias | 455-483 | Polar residues | ||||
Sequence: SGTPFGGSQGLPSPHPKAQLNTPLTFSQH | ||||||
Region | 455-515 | Disordered | ||||
Sequence: SGTPFGGSQGLPSPHPKAQLNTPLTFSQHLSKKRGPKPKEAFGGGGVGPPGAKKKSQKGKE | ||||||
Region | 577-660 | Disordered | ||||
Sequence: QGKKGRAGSANGAGSSLQQFQPHMATLSDFDSEDELQIDETPPPRRRPSLPSKKKLAGLPRKLPRAKPCSDPHRIREPGEVDFD | ||||||
Compositional bias | 587-602 | Polar residues | ||||
Sequence: NGAGSSLQQFQPHMAT | ||||||
Compositional bias | 642-657 | Basic and acidic residues | ||||
Sequence: AKPCSDPHRIREPGEV | ||||||
Region | 697-857 | Disordered | ||||
Sequence: LDSALSEEAPASPSTRDAIQGMLSMANPPSSSSSSSSSSPLSISGGGEMMGLMKEKGGREGWMSGVKKSERKAVFQRPGKRPIKRPARHLSDDESLDEQETLGTCFKDSDYVYPSLESDEEDHVSKSKMKRKRNWDDTPWSPKARVTPTLPKQERPVREGA | ||||||
Compositional bias | 713-740 | Polar residues | ||||
Sequence: DAIQGMLSMANPPSSSSSSSSSSPLSIS | ||||||
Compositional bias | 756-773 | Basic and acidic residues | ||||
Sequence: EGWMSGVKKSERKAVFQR | ||||||
Compositional bias | 781-800 | Basic and acidic residues | ||||
Sequence: RPARHLSDDESLDEQETLGT | ||||||
Compositional bias | 809-835 | Basic and acidic residues | ||||
Sequence: YPSLESDEEDHVSKSKMKRKRNWDDTP | ||||||
Region | 875-923 | Disordered | ||||
Sequence: QQEQQKTITKRKYTKKKTPQEKVHSTVAQLQHQPDSAPVSPPLPSEPPV | ||||||
Region | 943-1015 | Disordered | ||||
Sequence: EYTAGPGPFSPGGPRGSGAMAPGVFLTSRRPSLSPQNSSSYSPSAPSPGGLVTPTSAGACQGKRPKKGLATAK | ||||||
Compositional bias | 971-993 | Polar residues | ||||
Sequence: RRPSLSPQNSSSYSPSAPSPGGL |
Domain
The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 promotes its access to H3K9me2 (By similarity).
The linker region is a critical determinant of demethylase specificity. It enables the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3 (By similarity).
Sequence similarities
Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,032
- Mass (Da)114,222
- Last updated2010-10-05 v1
- ChecksumFD86E98931F75D94
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 455-483 | Polar residues | ||||
Sequence: SGTPFGGSQGLPSPHPKAQLNTPLTFSQH | ||||||
Compositional bias | 587-602 | Polar residues | ||||
Sequence: NGAGSSLQQFQPHMAT | ||||||
Compositional bias | 642-657 | Basic and acidic residues | ||||
Sequence: AKPCSDPHRIREPGEV | ||||||
Compositional bias | 713-740 | Polar residues | ||||
Sequence: DAIQGMLSMANPPSSSSSSSSSSPLSIS | ||||||
Compositional bias | 756-773 | Basic and acidic residues | ||||
Sequence: EGWMSGVKKSERKAVFQR | ||||||
Compositional bias | 781-800 | Basic and acidic residues | ||||
Sequence: RPARHLSDDESLDEQETLGT | ||||||
Compositional bias | 809-835 | Basic and acidic residues | ||||
Sequence: YPSLESDEEDHVSKSKMKRKRNWDDTP | ||||||
Compositional bias | 971-993 | Polar residues | ||||
Sequence: RRPSLSPQNSSSYSPSAPSPGGL |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
CR352210 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. |