Q5XUN4 · KDM5D_PANTR
- ProteinLysine-specific demethylase 5D
- GeneKDM5D
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids1535 (go to sequence)
- Protein existenceEvidence at transcript level
- Annotation score4/5
Function
function
Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks (By similarity).
Catalytic activity
- 3 2-oxoglutarate + N6,N6,N6-trimethyl-L-lysyl4-[histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl4-[histone H3] + 3 succinate
3 CHEBI:16810 + RHEA-COMP:15537 CHEBI:61961 Position: 4+ 3 CHEBI:15379 = 3 CHEBI:16526 + 3 CHEBI:16842 + RHEA-COMP:15547 + 3 CHEBI:30031
Cofactor
Protein has several cofactor binding sites:
Note: Binds 1 Fe2+ ion per subunit.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 430 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: Y | ||||||
Binding site | 504 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 506 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Binding site | 512 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: S | ||||||
Binding site | 514 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 522 | 2-oxoglutarate (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 592 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromatin | |
Cellular Component | nucleus | |
Molecular Function | DNA binding | |
Molecular Function | histone H3K4me/H3K4me2/H3K4me3 demethylase activity | |
Molecular Function | metal ion binding | |
Biological Process | chromatin remodeling | |
Biological Process | regulation of DNA-templated transcription |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLysine-specific demethylase 5D
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Pan
Accessions
- Primary accessionQ5XUN4
Proteomes
Subcellular Location
PTM/Processing
Features
Showing features for chain, cross-link, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000200590 | 1-1535 | Lysine-specific demethylase 5D | |||
Sequence: MEPGCNEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNFRFTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGANHVQCNTHPFDNEVKDKEYKPHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEEDIEKNPELKKLQIYGPGPKMMGLGLMAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTMQLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAECKQPPEAFGFEQATQEYTLQSFGEMADSFKSDYFNMPVHMVPTELLEKEFWRLVSSIEEDVTVEYGADIHYKEFGSGFPVSNSKQNLSPEEKEYATSGWNLNVMPVLAQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKMLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDLNLAVAVHKEMFIMVQEERRLRKALLEKGVTEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPTMLHKLKIRAESFDTWANKVRVALEVEDGRKRSFEELRALESEARERRFPNSELLQRLKNCLSEVEACIAQVLGLVSGQVARMDTPQLTLTELRVLLEQMGSLPCAMHQIGDVKDVLEQVEAYQDEAREALATLPSSPGLLRSLLERGQQLGVEVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASSPSVDKARAELQELLTIAERWEEKAHFCLEARQKHPPATLEAIIRETENIPVHLPNIQALKEALTKAQAWIADVDEIQNGDHYPCLDDLEGLVAVGRDLPVGLEELRQLELQVLTAHSWREKASKTFLKKNSCYTLLEVLCPCADAGSDSTKRSRWMEKALGLYQCDTELLGLSAQDLRDPGSLIVAFKEGEQKEKEGILQLRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGALQCDLCQDWFHGQCVSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLVALQRLPVRLPEGEALQCLTERAIGWQDRARKALASEDVTALLRHLAELRQQLQAKPRPVYTSATACDPIREGSGNNISKVQGLLENGDSVISPENMAPGKGSDLELLSSLLPQLTGPVLELPEAIRAPLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLDRIRTLLELEKFEHQGSRTRSRALERRRRQQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDHSPSLKGNQNSLQHKDSGSSAACPSLMPWLQLSYSDEQQL | ||||||
Cross-link | 205 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Cross-link | 229 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Cross-link | 244 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Cross-link | 272 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Modified residue | 291 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 307 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 884 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 1342 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
Interaction
Structure
Family & Domains
Features
Showing features for domain, region, compositional bias, zinc finger.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 14-55 | JmjN | ||||
Sequence: CPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPP | ||||||
Domain | 79-169 | ARID | ||||
Sequence: TRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQS | ||||||
Region | 192-227 | Disordered | ||||
Sequence: PHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEEDI | ||||||
Compositional bias | 197-211 | Polar residues | ||||
Sequence: LRQSVQPSKFSSYSR | ||||||
Compositional bias | 212-227 | Basic and acidic residues | ||||
Sequence: RAKRLQPDPEPTEEDI | ||||||
Zinc finger | 314-364 | PHD-type 1 | ||||
Sequence: SYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA | ||||||
Domain | 458-624 | JmjC | ||||
Sequence: EYATSGWNLNVMPVLAQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKMLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYNFAEAVNFCTADWLPAGRQCIEHYR | ||||||
Zinc finger | 697-749 | C5HC2 | ||||
Sequence: CIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPTM | ||||||
Zinc finger | 1174-1235 | PHD-type 2 | ||||
Sequence: ICVCGQVPAGVGALQCDLCQDWFHGQCVSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCM | ||||||
Region | 1425-1519 | Disordered | ||||
Sequence: HQGSRTRSRALERRRRQQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDHSPSLKGNQNSLQHKDSGSSAACP | ||||||
Compositional bias | 1447-1467 | Polar residues | ||||
Sequence: GRNVENLVQQELQSKRARSSG | ||||||
Compositional bias | 1474-1489 | Basic and acidic residues | ||||
Sequence: REEEHYQEKADRENMF | ||||||
Compositional bias | 1490-1519 | Polar residues | ||||
Sequence: LTPSTDHSPSLKGNQNSLQHKDSGSSAACP |
Domain
The JmjC domain is required for enzymatic activity.
Sequence similarities
Belongs to the JARID1 histone demethylase family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,535
- Mass (Da)173,743
- Last updated2004-11-23 v1
- ChecksumD1C6E59F8A02C435
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 197-211 | Polar residues | ||||
Sequence: LRQSVQPSKFSSYSR | ||||||
Compositional bias | 212-227 | Basic and acidic residues | ||||
Sequence: RAKRLQPDPEPTEEDI | ||||||
Compositional bias | 1447-1467 | Polar residues | ||||
Sequence: GRNVENLVQQELQSKRARSSG | ||||||
Compositional bias | 1474-1489 | Basic and acidic residues | ||||
Sequence: REEEHYQEKADRENMF | ||||||
Compositional bias | 1490-1519 | Polar residues | ||||
Sequence: LTPSTDHSPSLKGNQNSLQHKDSGSSAACP |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AY736376 EMBL· GenBank· DDBJ | AAU82116.1 EMBL· GenBank· DDBJ | mRNA |