Q91VY5 · KDM4B_MOUSE
- ProteinLysine-specific demethylase 4B
- GeneKdm4b
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids1086 (go to sequence)
- Protein existenceEvidence at transcript level
- Annotation score5/5
Function
function
Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate (By similarity).
Plays a critical role in the development of the central nervous system (CNS)
Plays a critical role in the development of the central nervous system (CNS)
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 | 133 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: Y | ||||||
Binding site | 189 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 191 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Binding site | 199 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 207 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 235 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 241 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 242 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 277 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 307 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 309 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromatin | |
Cellular Component | cytosol | |
Cellular Component | nucleoplasm | |
Cellular Component | nucleus | |
Cellular Component | pericentric heterochromatin | |
Molecular Function | histone demethylase activity | |
Molecular Function | histone H3K36 demethylase activity | |
Molecular Function | histone H3K9 demethylase activity | |
Molecular Function | histone H3K9me2/H3K9me3 demethylase activity | |
Molecular Function | metal ion binding | |
Biological Process | brain development | |
Biological Process | chromatin remodeling | |
Biological Process | regulation of gene expression |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLysine-specific demethylase 4B
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strain
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus
Accessions
- Primary accessionQ91VY5
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000183176 | 1-1086 | Lysine-specific demethylase 4B | |||
Sequence: MGSEDHSAQNPSCKIMTFRPTMDEFRDFNRYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPAPIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGSLYDDDVAQWNIGNLRTILDMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQCTCRKDMVKISMDVFVRILQPERYEQWKQGRDLTVLDHTRPTALSSPELSSWSASRTSIKAKLLRRQISVKESRPWRKAEEERRREPTRRPGPASHRRRSQPKKSKPEESRSPGEATAGVSTLDEARGCSRGEAMPEDEEEEELLPSQGHEAEGVEEDGRGKPRPTKARNKKKTPSPSSPPLLSAPPALFPTEEVLRPPPQPKSPGPAMGPMAAEGGPPPTPLNVVPPGAPVEEAEVRPRPIIPMLYVLPRTSSTDGDREHSAHAQLAPMELGPEEENQAQAGDSQGTTPFSKLKVEIKKSRRHPLGRPPTRSPLSVVKQEASSDEEAFLFSGEDDVTDPEALRSLLSLQWKNKAASFQAERKFNAAAALSEPYCAICTLFYPYSQSVQTERDSAVQPPSKSGQRTRPLIPEMCFTSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRCAAHAWTAECCLCNLRGGALQRTTEHRWIHVICAIAVPEVRFLNVIERNPVDVSAIPEQRWKLKCIYCRKRMKRVSGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWPYVVSITCLKHRASGAGGQLLRTVSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCLRLGPPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELPKRVRSRLSLSTGTPQEPSFSGDDVKAAKRPRVASVLATTTEDTGRSPEYLSFMESLLQAQGRPGAPF | ||||||
Modified residue | 599 | N6-acetyllysine | ||||
Sequence: K |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Developmental stage
Expression is especially strong in the hippocampus and throughout the CNS from embryonic periods through adulthood.
Gene expression databases
Structure
Family & Domains
Features
Showing features for domain, compositional bias, region, zinc finger.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 15-57 | JmjN | ||||
Sequence: IMTFRPTMDEFRDFNRYVAYIESQGAHRAGLAKIIPPKEWKPR | ||||||
Domain | 146-309 | JmjC | ||||
Sequence: VAQWNIGNLRTILDMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATLRWIDYGKVATQCTC | ||||||
Compositional bias | 379-395 | Basic and acidic residues | ||||
Sequence: SRPWRKAEEERRREPTR | ||||||
Region | 379-536 | Disordered | ||||
Sequence: SRPWRKAEEERRREPTRRPGPASHRRRSQPKKSKPEESRSPGEATAGVSTLDEARGCSRGEAMPEDEEEEELLPSQGHEAEGVEEDGRGKPRPTKARNKKKTPSPSSPPLLSAPPALFPTEEVLRPPPQPKSPGPAMGPMAAEGGPPPTPLNVVPPGA | ||||||
Compositional bias | 453-470 | Basic and acidic residues | ||||
Sequence: SQGHEAEGVEEDGRGKPR | ||||||
Compositional bias | 485-533 | Pro residues | ||||
Sequence: SPPLLSAPPALFPTEEVLRPPPQPKSPGPAMGPMAAEGGPPPTPLNVVP | ||||||
Region | 557-624 | Disordered | ||||
Sequence: RTSSTDGDREHSAHAQLAPMELGPEEENQAQAGDSQGTTPFSKLKVEIKKSRRHPLGRPPTRSPLSVV | ||||||
Zinc finger | 719-777 | PHD-type 1 | ||||
Sequence: MCFTSSGENTEPLPANSYVGEDGTSPLISCAHCCLQVHASCYGVRPELAKEGWTCSRCA | ||||||
Zinc finger | 782-815 | C2HC pre-PHD-type | ||||
Sequence: TAECCLCNLRGGALQRTTEHRWIHVICAIAVPEV | ||||||
Zinc finger | 838-895 | PHD-type 2 | ||||
Sequence: LKCIYCRKRMKRVSGACIQCSYEHCSTSFHVTCAHAAGVLMEPDDWPYVVSITCLKHR | ||||||
Domain | 905-962 | Tudor 1 | ||||
Sequence: RTVSLGQIVITKNRNGLYYRCRVIGTTAQTFYEVNFDDGSYSDNLYPESITSRDCLRL | ||||||
Domain | 963-1019 | Tudor 2 | ||||
Sequence: GPPPEGELVELRWTDGNLYRARFISMATSLIYQVEFEDGSQLTVKRGDIFTLEEELP | ||||||
Region | 1024-1043 | Disordered | ||||
Sequence: SRLSLSTGTPQEPSFSGDDV |
Domain
The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).
Sequence similarities
Belongs to the JHDM3 histone demethylase family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence & Isoform
- Sequence statusComplete
This entry describes 2 isoforms produced by Alternative splicing.
Q91VY5-1
This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
- Name1
- Length1,086
- Mass (Da)121,604
- Last updated2001-12-01 v1
- Checksum5418B6CBF5E14DAA
Q91VY5-2
- Name2
Computationally mapped potential isoform sequences
There are 3 potential isoforms mapped to this entry
Sequence caution
Features
Showing features for sequence conflict, compositional bias, alternative sequence.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 40 | in Ref. 1; BAE24866 | ||||
Sequence: A → T | ||||||
Compositional bias | 379-395 | Basic and acidic residues | ||||
Sequence: SRPWRKAEEERRREPTR | ||||||
Compositional bias | 453-470 | Basic and acidic residues | ||||
Sequence: SQGHEAEGVEEDGRGKPR | ||||||
Compositional bias | 485-533 | Pro residues | ||||
Sequence: SPPLLSAPPALFPTEEVLRPPPQPKSPGPAMGPMAAEGGPPPTPLNVVP | ||||||
Sequence conflict | 576 | in Ref. 2; AAH05480 | ||||
Sequence: M → L | ||||||
Alternative sequence | VSP_018309 | 593-599 | in isoform 2 | |||
Sequence: Missing | ||||||
Alternative sequence | VSP_018310 | 940-997 | in isoform 2 | |||
Sequence: Missing |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AK129233 EMBL· GenBank· DDBJ | BAC98043.1 EMBL· GenBank· DDBJ | mRNA | Different initiation | |
AK141879 EMBL· GenBank· DDBJ | BAE24866.1 EMBL· GenBank· DDBJ | mRNA | ||
BC005480 EMBL· GenBank· DDBJ | AAH05480.1 EMBL· GenBank· DDBJ | mRNA | ||
BC007145 EMBL· GenBank· DDBJ | AAH07145.1 EMBL· GenBank· DDBJ | mRNA |