F4KIX0 · JMJ13_ARATH
- ProteinLysine-specific demethylase JMJ13
- GeneJMJ13
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids787 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and involved in the regulation of gene expression (PubMed:30899015).
Acts as a temperature and photoperiod dependent flowering repressor (PubMed:30899015).
Acts as a temperature and photoperiod dependent flowering repressor (PubMed:30899015).
Catalytic activity
- 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl27-[histone H3] + O2 = CO2 + formaldehyde + N6,N6-dimethyl-L-lysyl27-[histone H3] + succinateThis reaction proceeds in the forward direction.
CHEBI:16810 + RHEA-COMP:15535 CHEBI:61961 Position: 27+ CHEBI:15379 = CHEBI:16526 + CHEBI:16842 + RHEA-COMP:15539 CHEBI:61976 Position: 27+ CHEBI:30031
Cofactor
Note: Binds 1 Fe2+ ion per subunit.
Features
Showing features for site, binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Site | 179 | Histone H3 binding | ||||
Sequence: F | ||||||
Site | 236 | Histone H3 binding | ||||
Sequence: D | ||||||
Site | 282 | Histone H3 binding | ||||
Sequence: Y | ||||||
Binding site | 293 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 295 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Site | 296 | Histone H3 binding | ||||
Sequence: D | ||||||
Binding site | 388 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Site | 402 | Histone H3 binding | ||||
Sequence: N | ||||||
Binding site | 500 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 503 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 514 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 516 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 519 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 522 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 525 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 534 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | nucleus | |
Molecular Function | DNA-binding transcription factor activity | |
Molecular Function | histone binding | |
Molecular Function | histone demethylase activity | |
Molecular Function | histone H3K27me2/H3K27me3 demethylase activity | |
Molecular Function | metal ion binding | |
Biological Process | flower development | |
Biological Process | long-day photoperiodism | |
Biological Process | negative regulation of gene expression, epigenetic | |
Biological Process | negative regulation of long-day photoperiodism, flowering | |
Biological Process | negative regulation of short-day photoperiodism, flowering | |
Biological Process | regulation of DNA-templated transcription | |
Biological Process | response to temperature stimulus |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLysine-specific demethylase JMJ13
- EC number
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionF4KIX0
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
Subcellular Location
Phenotypes & Variants
Disruption phenotype
Early flowering in both long and short days conditions, but in a temperature sensitive manner only in short days.
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 179 | Strongly reduced demethylase activity. | ||||
Sequence: F → N | ||||||
Mutagenesis | 179 | Slightly reduced demethylase activity. | ||||
Sequence: F → S | ||||||
Mutagenesis | 236 | Impaired demethylase activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 282 | Impaired demethylase activity. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 295 | Impaired demethylase activity. | ||||
Sequence: E → A | ||||||
Mutagenesis | 296 | Impaired demethylase activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 388 | Impaired demethylase activity. | ||||
Sequence: H → A | ||||||
Mutagenesis | 402 | Impaired demethylase activity. | ||||
Sequence: N → A |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 42 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000456188 | 1-787 | Lysine-specific demethylase JMJ13 | |||
Sequence: MAERRICLSKEAKDGLEFLKRKKLQKMRSDSVNETVGFSTMARSGGDALRPTSASCGMRLRVTSSDTVSKVHGASTVRGGLMKEKVEKLETDDLKWTERLPECPVYRPTKEEFEDPLTYLQKIFPEASKYGICKIVSPLTATVPAGAVLMKEKSNFKFTTRVQPLRLAEWDSDDKVTFFMSGRTYTFRDYEKMANKVFARRYCSGGSLPDSFLEKEFWKEIACGKTETVEYACDVDGSAFSSAPGDPLGSSKWNLNKVSRLPKSTLRLLETSIPGVTEPMLYIGMLFSMFAWHVEDHYLYSINYQHCGASKTWYGIPGSAALKFEKVVKECVYNDDILSTNGEDGAFDVLLGKTTIFPPKTLLDHNVPVYKAVQKPGEFVVTFPRAYHAGFSHGFNCGEAVNFAMGDWFPFGAIASCRYAHLNRVPLLPHEELICKEAMLLNSSSKSENLDLTPTELSGQRSIKTAFVHLIRFLHLARWSLMKSGLCTGLVSNTYGTIVCSLCKRDCYLAFINCECYSHPVCLRHDVKKLDLPCGTTHTLYLRDNIEDMEAAAMKFEKEDGVSDLITTDEDLYKYPSSITLPAAKEDGYTPYSTIYFDFYTEVEMTSHDQLQSGNPVMSYEANASCISSVADDYECSDYVNRRANCSSSSDSKLSEEVACSSSKKTRFFPVVQDEQLVADQESDGSDSECFRVKRRSSLKFENRTVVLDTRESDHHQELKRLKKSHHHEGRYSSSSSVSRQEEEEDELVISNRKETQQQSDVKMQKKRIENHFGGFKRLKVKGLIKP |
Proteomic databases
PTM databases
Expression
Tissue specificity
Mostly expressed in leaves, and, to a lower extent, in inflorescences, roots, siliques and stems.
Induction
Accumulates in response to higher temperature and during long days (at protein level).
Gene expression databases
Interaction
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for domain, zinc finger, region, compositional bias, motif.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 103-144 | JmjN | ||||
Sequence: CPVYRPTKEEFEDPLTYLQKIFPEASKYGICKIVSPLTATVP | ||||||
Domain | 250-420 | JmjC | ||||
Sequence: SSKWNLNKVSRLPKSTLRLLETSIPGVTEPMLYIGMLFSMFAWHVEDHYLYSINYQHCGASKTWYGIPGSAALKFEKVVKECVYNDDILSTNGEDGAFDVLLGKTTIFPPKTLLDHNVPVYKAVQKPGEFVVTFPRAYHAGFSHGFNCGEAVNFAMGDWFPFGAIASCRYA | ||||||
Zinc finger | 500-551 | C4HCHC | ||||
Sequence: CSLCKRDCYLAFINCECYSHPVCLRHDVKKLDLPCGTTHTLYLRDNIEDMEA | ||||||
Zinc finger | 500-551 | C5HC2 | ||||
Sequence: CSLCKRDCYLAFINCECYSHPVCLRHDVKKLDLPCGTTHTLYLRDNIEDMEA | ||||||
Domain | 617-675 | FYR N-terminal | ||||
Sequence: VMSYEANASCISSVADDYECSDYVNRRANCSSSSDSKLSEEVACSSSKKTRFFPVVQDE | ||||||
Domain | 677-756 | FYR C-terminal | ||||
Sequence: LVADQESDGSDSECFRVKRRSSLKFENRTVVLDTRESDHHQELKRLKKSHHHEGRYSSSSSVSRQEEEEDELVISNRKET | ||||||
Region | 712-769 | Disordered | ||||
Sequence: ESDHHQELKRLKKSHHHEGRYSSSSSVSRQEEEEDELVISNRKETQQQSDVKMQKKRI | ||||||
Compositional bias | 729-752 | Basic and acidic residues | ||||
Sequence: EGRYSSSSSVSRQEEEEDELVISN | ||||||
Motif | 752-759 | Nuclear localization signal | ||||
Sequence: NRKETQQQ |
Sequence similarities
Belongs to the JARID1 histone demethylase family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length787
- Mass (Da)88,821
- Last updated2011-06-28 v1
- Checksum0313F217FEF3FF94
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A0A1P8BAS6 | A0A1P8BAS6_ARATH | JMJ13 | 646 |
Sequence caution
Features
Showing features for sequence conflict, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 639 | in Ref. 1; BAB10230 | ||||
Sequence: Y → YQ | ||||||
Compositional bias | 729-752 | Basic and acidic residues | ||||
Sequence: EGRYSSSSSVSRQEEEEDELVISN |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AB013394 EMBL· GenBank· DDBJ | BAB10230.1 EMBL· GenBank· DDBJ | Genomic DNA | Sequence problems. | |
CP002688 EMBL· GenBank· DDBJ | AED95446.1 EMBL· GenBank· DDBJ | Genomic DNA |