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IID00009
 UniprotO60341
ProteinLysine-specific histone demethylase 1A
GeneKDM1A
OrganismHomo sapiens
Sequence LLPS PhaSepDB
PhaSePro
LLPSDB
DrLLPS Network xml rdf
Structure
Experiment
  :order   disorder   conflict   PDB cluster   ProS   Pfam Domain   SEG
852
 order/disorder by at least rule
     disorder by at least rule
     order by at least rule
 order/disorder by majority rule
Seq 1-852 Hetero dimer : IID00422Complex
 Evidence X-RAY 2uxx A Reference
       Region 2uxx A 171-835 order
       Region 2uxx A 836-836 disorder
 Evidence X-RAY 4uvb A Reference
       Region 4uvb A 1-170 disorder
       Region 4uvb A 171-836 order
       Region 4uvb A 837-852 disorder
 Evidence X-RAY 5lhi A Reference
       Region 5lhi A 1-170 disorder
       Region 5lhi A 171-836 order
       Region 5lhi A 837-852 disorder
 Evidence X-RAY 5lhh A Reference
       Region 5lhh A 1-170 disorder
       Region 5lhh A 171-836 order
       Region 5lhh A 837-852 disorder
 Evidence X-RAY 5lhg A Reference
       Region 5lhg A 1-170 disorder
       Region 5lhg A 171-836 order
       Region 5lhg A 837-852 disorder
 Evidence X-RAY 5lgu A Reference
       Region 5lgu A 123-170 disorder
       Region 5lgu A 171-836 order
       Region 5lgu A 837-852 disorder
 Evidence X-RAY 5lgt A Reference
       Region 5lgt A 123-170 disorder
       Region 5lgt A 171-836 order
       Region 5lgt A 837-852 disorder
 Evidence X-RAY 5lgn A Reference
       Region 5lgn A 172-836 order
 Evidence X-RAY 5lbq A Reference
       Region 5lbq A 123-170 disorder
       Region 5lbq A 171-836 order
       Region 5lbq A 837-852 disorder
 Evidence X-RAY 2xas A Reference
       Region 2xas A 1-170 disorder
       Region 2xas A 171-836 order
       Region 2xas A 837-852 disorder
 Evidence X-RAY 2xaq A Reference
       Region 2xaq A 1-170 disorder
       Region 2xaq A 171-836 order
       Region 2xaq A 837-852 disorder
 Evidence X-RAY 2xaj A Reference
       Region 2xaj A 1-170 disorder
       Region 2xaj A 171-836 order
       Region 2xaj A 837-852 disorder
 Evidence X-RAY 2xah A Reference
       Region 2xah A 1-170 disorder
       Region 2xah A 171-836 order
       Region 2xah A 837-852 disorder
 Evidence X-RAY 2xag A Reference
       Region 2xag A 1-170 disorder
       Region 2xag A 171-836 order
       Region 2xag A 837-852 disorder
 Evidence X-RAY 2xaf A Reference
       Region 2xaf A 1-170 disorder
       Region 2xaf A 171-836 order
       Region 2xaf A 837-852 disorder
 Evidence X-RAY 4uxn A Reference
       Region 4uxn A 1-170 disorder
       Region 4uxn A 171-836 order
       Region 4uxn A 837-852 disorder
 Evidence X-RAY 4uvc A Reference
       Region 4uvc A 1-170 disorder
       Region 4uvc A 171-836 order
       Region 4uvc A 837-852 disorder
 Evidence X-RAY 4uva A Reference
       Region 4uva A 1-170 disorder
       Region 4uva A 171-836 order
       Region 4uva A 837-852 disorder
 Evidence X-RAY 4uv9 A Reference
       Region 4uv9 A 1-170 disorder
       Region 4uv9 A 171-836 order
       Region 4uv9 A 837-852 disorder
 Evidence X-RAY 4uv8 A Reference
       Region 4uv8 A 1-170 disorder
       Region 4uv8 A 171-836 order
       Region 4uv8 A 837-852 disorder
 Evidence X-RAY 5l3g A Reference
       Region 5l3g A 123-170 disorder
       Region 5l3g A 171-836 order
       Region 5l3g A 837-852 disorder
 Evidence X-RAY 5l3f A Reference
       Region 5l3f A 123-170 disorder
       Region 5l3f A 171-836 order
       Region 5l3f A 837-852 disorder
 Evidence X-RAY 5l3e A Reference
       Region 5l3e A 123-170 disorder
       Region 5l3e A 171-836 order
       Region 5l3e A 837-852 disorder
 Evidence X-RAY 5l3d A Reference
       Region 5l3d A 1-170 disorder
       Region 5l3d A 171-836 order
       Region 5l3d A 837-852 disorder
 Evidence X-RAY 5l3c A Reference
       Region 5l3c A 1-170 disorder
       Region 5l3c A 171-836 order
       Region 5l3c A 837-852 disorder
 Evidence X-RAY 5l3b A Reference
       Region 5l3b A 1-170 disorder
       Region 5l3b A 171-836 order
       Region 5l3b A 837-852 disorder
 Evidence X-RAY 4kum A Reference
       Region 4kum A 171-836 order
 Evidence X-RAY 2iw5 A Reference
       Region 2iw5 A 171-836 order
 Evidence X-RAY 4bay A Reference
       Region 4bay A 172-836 order
       Region 4bay A 837-852 disorder
Seq 1-852 Hetero trimer : IID00422Complex
 Evidence X-RAY 3zmt A Reference
       Region 3zmt A 1-171 disorder
       Region 3zmt A 172-836 order
       Region 3zmt A 837-852 disorder
Seq 1-852 Hetero trimer : IID00422Complex
 Evidence X-RAY 3zn0 A Reference
       Region 3zn0 A 1-170 disorder
       Region 3zn0 A 171-836 order
       Region 3zn0 A 837-852 disorder
Seq 1-852 Hetero trimer : IID00422Complex
 Evidence X-RAY 3zmu A Reference
       Region 3zmu A 1-171 disorder
       Region 3zmu A 172-836 order
       Region 3zmu A 837-852 disorder
Seq 1-852 Hetero trimer : IID00415Complex,IID00422Complex
 Evidence X-RAY 3zms A Reference
       Region 3zms A 1-171 disorder
       Region 3zms A 172-836 order
       Region 3zms A 837-852 disorder
Seq 1-852 Hetero trimer : IID00422Complex
 Evidence X-RAY 3zmz A Reference
       Region 3zmz A 1-170 disorder
       Region 3zmz A 171-836 order
       Region 3zmz A 837-852 disorder
Seq 1-852 Hetero dimer : IID00589Complex
 Evidence X-RAY 4czz A Reference
       Region 4czz A 1-170 disorder
       Region 4czz A 171-836 order
       Region 4czz A 837-852 disorder
Seq 1-852 Hetero trimer : IID00422Complex
 Evidence X-RAY 3zn1 A Reference
       Region 3zn1 A 1-170 disorder
       Region 3zn1 A 171-836 order
       Region 3zn1 A 837-852 disorder
Seq 1-852 Hetero tetramer : IID00422Complex
 Evidence X-RAY 3zmv A Reference
       Region 3zmv A 1-171 disorder
       Region 3zmv A 172-836 order
       Region 3zmv A 837-852 disorder
Seq 108-119 Hetero dimer : IID00003Complex
 Evidence X-RAY 5afw B Reference
       Region 5afw B 108-109 disorder
       Region 5afw B 110-116 order
       Region 5afw B 117-119 disorder
Seq 123-852 Hetero trimer : IID00363Complex,IID00422Complex
 Evidence X-RAY 2y48 A Reference
       Region 2y48 A 123-171 disorder
       Region 2y48 A 172-836 order
       Region 2y48 A 837-852 disorder
Seq 123-852 Hetero trimer : IID00086Complex,IID00422Complex
 Evidence X-RAY 2v1d A Reference
       Region 2v1d A 123-170 disorder
       Region 2v1d A 171-836 order
       Region 2v1d A 837-852 disorder
Seq 123-852 Hetero trimer : IID00062Complex,IID00422Complex
 Evidence X-RAY 5x60 A Reference
       Region 5x60 A 172-833 order
 Evidence X-RAY 2x0l A Reference
       Region 2x0l A 123-170 disorder
       Region 2x0l A 171-836 order
       Region 2x0l A 837-852 disorder
 Evidence X-RAY 5h6r A Reference
       Region 5h6r A 172-833 order
 Evidence X-RAY 5h6q A Reference
       Region 5h6q A 172-832 order
       Region 5h6q A 833-833 disorder
Seq 169-279 Monomer :
 Evidence NMR 2com A Reference
       Region 2com A 169-279 order
       Region 2com A 169-170 high_rmsd
       Region 2com A 270-279 high_rmsd
 Evidence NMR 2l3d A Reference
       Region 2l3d A 174-273 order
       Region 2l3d A 174-179 high_rmsd
       Region 2l3d A 263-273 high_rmsd
Seq 171-836 Hetero octamer : IID00422Complex
 Evidence X-RAY 4xbf A Reference
       Region 4xbf A 171-836 order
Seq 171-836 Hetero trimer : IID00062Complex,IID00422Complex
 Evidence X-RAY 2uxn A Reference
       Region 2uxn A 171-172 disorder
       Region 2uxn A 173-836 order
Seq 172-835 Monomer :
 Evidence X-RAY 2z5u A Reference
       Region 2z5u A 172-464 order
       Region 2z5u A 465-473 disorder
       Region 2z5u A 474-782 order
       Region 2z5u A 783-791 disorder
       Region 2z5u A 792-831 order
       Region 2z5u A 832-833 disorder
 Evidence X-RAY 2z3y A Reference
       Region 2z3y A 172-464 order
       Region 2z3y A 465-472 disorder
       Region 2z3y A 473-782 order
       Region 2z3y A 783-791 disorder
       Region 2z3y A 792-831 order
       Region 2z3y A 832-833 disorder
 Evidence X-RAY 2hko A Reference
       Region 2hko A 172-172 disorder
       Region 2hko A 173-465 order
       Region 2hko A 466-473 disorder
       Region 2hko A 474-785 order
       Region 2hko A 786-790 disorder
       Region 2hko A 791-832 order
       Region 2hko A 833-835 disorder
 Evidence X-RAY 2h94 A Reference
       Region 2h94 A 172-466 order
       Region 2h94 A 467-474 disorder
       Region 2h94 A 475-783 order
       Region 2h94 A 784-792 disorder
       Region 2h94 A 793-835 order
 Evidence X-RAY 2ejr A Reference
       Region 2ejr A 172-464 order
       Region 2ejr A 465-472 disorder
       Region 2ejr A 473-782 order
       Region 2ejr A 783-791 disorder
       Region 2ejr A 792-831 order
       Region 2ejr A 832-833 disorder
 Evidence X-RAY 2dw4 A Reference
       Region 2dw4 A 172-459 order
       Region 2dw4 A 460-474 disorder
       Region 2dw4 A 475-697 order
       Region 2dw4 A 698-699 disorder
       Region 2dw4 A 700-782 order
       Region 2dw4 A 783-791 disorder
       Region 2dw4 A 792-831 order
 Evidence X-RAY 3abu A Reference
       Region 3abu A 172-464 order
       Region 3abu A 465-473 disorder
       Region 3abu A 474-782 order
       Region 3abu A 783-791 disorder
       Region 3abu A 792-833 order
 Evidence X-RAY 3abt A Reference
       Region 3abt A 172-464 order
       Region 3abt A 465-472 disorder
       Region 3abt A 473-782 order
       Region 3abt A 783-791 disorder
       Region 3abt A 792-831 order
       Region 3abt A 832-833 disorder
Seq 183-267 Homo dimer :
 Evidence X-RAY 5it3 B Reference
       Region 5it3 B 183-267 order
 Evidence X-RAY 5it3 A Reference
       Region 5it3 A 183-267 order
SeqProS verified 110-116 Hetero dimer : IID00003Complex
       Region 5afw B 110-116 order
       Region 2xaj A 1-170 disorder
SeqProS verified 467-474 Hetero octamer : IID00422Complex
       Region 4xbf A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00422Complex
       Region 3zn1 A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00062Complex,IID00422Complex
       Region 2x0l A 171-836 order
       Region 5h6q A 172-832 order
       Region 5x60 A 172-833 order
       Region 5h6r A 172-833 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00062Complex,IID00422Complex
       Region 2uxn A 173-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero dimer : IID00589Complex
       Region 4czz A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00422Complex
       Region 3zn0 A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00363Complex,IID00422Complex
       Region 2y48 A 172-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero dimer : IID00422Complex
       Region 2xaj A 171-836 order
       Region 2xaq A 171-836 order
       Region 2iw5 A 171-836 order
       Region 2xas A 171-836 order
       Region 2uxx A 171-835 order
       Region 2xaf A 171-836 order
       Region 2xag A 171-836 order
       Region 2xah A 171-836 order
       Region 4bay A 172-836 order
       Region 4kum A 171-836 order
       Region 4uv8 A 171-836 order
       Region 4uv9 A 171-836 order
       Region 4uva A 171-836 order
       Region 4uxn A 171-836 order
       Region 4uvb A 171-836 order
       Region 4uvc A 171-836 order
       Region 5l3e A 171-836 order
       Region 5l3g A 171-836 order
       Region 5lhh A 171-836 order
       Region 5lgu A 171-836 order
       Region 5l3c A 171-836 order
       Region 5lgn A 172-836 order
       Region 5lgt A 171-836 order
       Region 5lhi A 171-836 order
       Region 5l3f A 171-836 order
       Region 5l3d A 171-836 order
       Region 5lhg A 171-836 order
       Region 5lbq A 171-836 order
       Region 5l3b A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00415Complex,IID00422Complex
       Region 3zms A 172-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00422Complex
       Region 3zmu A 172-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00422Complex
       Region 3zmt A 172-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00086Complex,IID00422Complex
       Region 2v1d A 171-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero tetramer : IID00422Complex
       Region 3zmv A 172-836 order
       Region 2dw4 A 460-474 disorder
SeqProS verified 467-474 Hetero trimer : IID00422Complex
       Region 3zmz A 171-836 order
       Region 2dw4 A 460-474 disorder
Seqphosphorylation
    611-611 Phosphoserine
    849-849 Phosphoserine
    166-166 Phosphoserine
    137-137 Phosphoserine
    135-135 Phosphotyrosine
    131-131 Phosphoserine
    126-126 Phosphoserine
    104-104 Phosphothreonine
    59-59 Phosphothreonine
 
Prediction
NeProc
Disorder 1-166,425-431,784-788,838-852
Order 167-424,432-783,793-837
ProS 33-40,117-134,166-166,425-431
AlphaFold
Disorder 1-169,838-852
Order 170-837
Pfam Hmmer
PF04433 174-264 3.3e-23
PF01593 288-826 2.5e-124
SEG 7-30 ,138-171 ,275-290 ,499-512 ,759-770
Function
Function in SwissProt
Histone demethylase that can demethylate both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context (PubMed:15620353, PubMed:15811342, PubMed:16140033, PubMed:16079794, PubMed:16079795, PubMed:16223729). Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed (PubMed:15620353, PubMed:15811342, PubMed:16079794, PubMed:21300290). Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me (PubMed:15620353, PubMed:20389281, PubMed:21300290, PubMed:23721412). May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity (PubMed:16140033, PubMed:16079794, PubMed:16885027, PubMed:21300290, PubMed:23721412). Also acts as a coactivator of androgen receptor (AR)-dependent transcription, by being recruited to AR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in AR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A (PubMed:16079795). Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7 (PubMed:20389281).
Biological Process
See also
Diagram with PDB data
REST/Sin3bSolution structure of the NRSF/REST-mSin3B PAH1 complex