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O60341

- KDM1A_HUMAN

UniProt

O60341 - KDM1A_HUMAN

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Protein

Lysine-specific histone demethylase 1A

Gene

KDM1A

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. 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. 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. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-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. 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 CDN7.6 Publications

Cofactori

FAD.2 Publications

Kineticsi

  1. KM=3.0 µM for H3 monomethyl-K41 Publication
  2. KM=4.2 µM for H3 dimethyl-K41 Publication
  3. KM=3.9 µM for H3 monomethyl-K4-monomethyl-K91 Publication
  4. KM=17.5 µM for monomethyl-K4-acetyl-K91 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei289 – 2891FAD2 Publications
Binding sitei308 – 3081FAD2 Publications
Binding sitei310 – 3101FAD2 Publications
Binding sitei316 – 3161FAD2 Publications
Binding sitei801 – 8011FAD2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi281 – 30929FADSequence AnalysisAdd
BLAST
Nucleotide bindingi332 – 3332FAD2 Publications
Nucleotide bindingi810 – 8112FAD2 Publications

GO - Molecular functioni

  1. androgen receptor binding Source: UniProtKB
  2. chromatin binding Source: UniProtKB
  3. demethylase activity Source: BHF-UCL
  4. enzyme binding Source: BHF-UCL
  5. flavin adenine dinucleotide binding Source: UniProtKB
  6. histone demethylase activity Source: BHF-UCL
  7. histone demethylase activity (H3-dimethyl-K4 specific) Source: UniProtKB
  8. histone demethylase activity (H3-K4 specific) Source: UniProtKB
  9. histone demethylase activity (H3-K9 specific) Source: UniProtKB
  10. ligand-dependent nuclear receptor transcription coactivator activity Source: UniProtKB
  11. MRF binding Source: BHF-UCL
  12. oxidoreductase activity Source: UniProtKB
  13. p53 binding Source: BHF-UCL
  14. sequence-specific DNA binding transcription factor activity Source: Ensembl
  15. transcription factor binding Source: BHF-UCL
  16. transcription regulatory region DNA binding Source: BHF-UCL

GO - Biological processi

  1. blood coagulation Source: Reactome
  2. cell proliferation Source: Ensembl
  3. granulocyte differentiation Source: Ensembl
  4. histone H3-K4 demethylation Source: UniProtKB
  5. histone H3-K9 demethylation Source: UniProtKB
  6. in utero embryonic development Source: Ensembl
  7. muscle cell development Source: BHF-UCL
  8. negative regulation of DNA binding Source: BHF-UCL
  9. negative regulation of DNA damage response, signal transduction by p53 class mediator Source: BHF-UCL
  10. negative regulation of histone H3-K4 methylation Source: Ensembl
  11. negative regulation of histone H3-K9 methylation Source: Ensembl
  12. negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator Source: BHF-UCL
  13. negative regulation of protein binding Source: BHF-UCL
  14. negative regulation of sequence-specific DNA binding transcription factor activity Source: BHF-UCL
  15. negative regulation of transcription, DNA-templated Source: BHF-UCL
  16. negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  17. pituitary gland development Source: Ensembl
  18. positive regulation of erythrocyte differentiation Source: Ensembl
  19. positive regulation of hormone biosynthetic process Source: Ensembl
  20. positive regulation of megakaryocyte differentiation Source: Ensembl
  21. positive regulation of neural precursor cell proliferation Source: Ensembl
  22. positive regulation of sequence-specific DNA binding transcription factor activity Source: BHF-UCL
  23. positive regulation of stem cell proliferation Source: Ensembl
  24. positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  25. protein demethylation Source: BHF-UCL
  26. regulation of primitive erythrocyte differentiation Source: Ensembl
  27. regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  28. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Oxidoreductase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

FAD, Flavoprotein

Enzyme and pathway databases

ReactomeiREACT_24970. Factors involved in megakaryocyte development and platelet production.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific histone demethylase 1A (EC:1.-.-.-)
Alternative name(s):
BRAF35-HDAC complex protein BHC110
Flavin-containing amine oxidase domain-containing protein 2
Gene namesi
Name:KDM1A
Synonyms:AOF2, KDM1, KIAA0601, LSD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:29079. KDM1A.

Subcellular locationi

Nucleus 2 Publications

GO - Cellular componenti

  1. nuclear chromatin Source: BHF-UCL
  2. nucleoplasm Source: Reactome
  3. nucleus Source: UniProtKB
  4. transcription factor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi535 – 5351N → A: Strongly reduces demethylase activity. 1 Publication
Mutagenesisi564 – 5641H → A: Strongly reduces demethylase activity. 1 Publication
Mutagenesisi661 – 6611K → A: Abolishes histone demethylase activity. 1 Publication
Mutagenesisi761 – 7611Y → A: Strongly reduces demethylase activity. 1 Publication

Organism-specific databases

PharmGKBiPA165751392.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 852852Lysine-specific histone demethylase 1APRO_0000099881Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei104 – 1041Phosphothreonine2 Publications
Modified residuei126 – 1261Phosphoserine1 Publication
Modified residuei131 – 1311Phosphoserine7 Publications
Modified residuei137 – 1371Phosphoserine3 Publications
Modified residuei166 – 1661Phosphoserine4 Publications
Modified residuei849 – 8491Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO60341.
PaxDbiO60341.
PRIDEiO60341.

PTM databases

PhosphoSiteiO60341.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiO60341.
CleanExiHS_AOF2.
ExpressionAtlasiO60341. baseline and differential.
GenevestigatoriO60341.

Organism-specific databases

HPAiCAB005884.
HPA053660.

Interactioni

Subunit structurei

Component of a RCOR/GFI/KDM1A/HDAC complex. Interacts directly with GFI1 and GFI1B. Interacts with INSM1 By similarity. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it from the proteasome while PHF21A/BHC80 inhibits the demethylase activity. Interacts with the androgen receptor (AR). Interacts with ASXL1. Interacts with SNAI1 (via SNAG domain).By similarity10 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
AKAP9Q999962EBI-710124,EBI-1048311
ASXL1Q8IXJ92EBI-710124,EBI-1646500
Asxl1P595982EBI-710124,EBI-5743705From a different organism.
C8orf74Q6P0472EBI-710124,EBI-8466055
CCDC151A5D8V72EBI-710124,EBI-8466445
CDCA4Q9BXL82EBI-710124,EBI-1773949
CEP70Q8NHQ12EBI-710124,EBI-739624
CHD3Q128734EBI-710124,EBI-523590
DNAJA3Q96EY12EBI-710124,EBI-356767
FAM9AQ8IZU12EBI-710124,EBI-8468186
FYCO1Q9BQS82EBI-710124,EBI-2869338
GSTCDQ8NEC72EBI-710124,EBI-8469616
GTPBP2Q9BX102EBI-710124,EBI-6115579
HAUS1Q96CS22EBI-710124,EBI-2514791
HDAC3O153794EBI-710124,EBI-607682
HESX1Q9UBX02EBI-710124,EBI-8470369
HIST3H3Q166952EBI-710124,EBI-358900
IMMTQ168912EBI-710124,EBI-473801
KLHDC4Q8TBB52EBI-710124,EBI-8472352
LOXL4Q96JB62EBI-710124,EBI-749562
MBD3O959834EBI-710124,EBI-1783068
NR1H3Q131332EBI-710124,EBI-781356
OFCC1Q8IZS52EBI-710124,EBI-8477661
PELP1Q8IZL86EBI-710124,EBI-716449
PHF19Q5T6S32EBI-710124,EBI-2339674
PPARDQ031812EBI-710124,EBI-6426768
PSMC1P621912EBI-710124,EBI-357598
RASSF1Q9NS232EBI-710124,EBI-367363
RASSF2P507492EBI-710124,EBI-960081
RCOR1Q9UKL05EBI-710124,EBI-926563
SAMD3Q8N6K72EBI-710124,EBI-748741
SERGEFQ9UGK82EBI-710124,EBI-465368
SF3B2Q134352EBI-710124,EBI-749111
SMAD9O151982EBI-710124,EBI-748763
SNAI1O9586332EBI-710124,EBI-1045459
SNF8Q96H202EBI-710124,EBI-747719
SPSB1Q96BD62EBI-710124,EBI-2659201
STX19Q8N4C72EBI-710124,EBI-8484990

Protein-protein interaction databases

BioGridi116667. 286 interactions.
DIPiDIP-34641N.
IntActiO60341. 217 interactions.
MINTiMINT-1372817.

Structurei

Secondary structure

1
852
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi173 – 1808
Beta strandi181 – 1833
Beta strandi185 – 1873
Helixi190 – 1956
Helixi197 – 2004
Helixi204 – 22219
Helixi231 – 2377
Helixi242 – 2443
Helixi246 – 25813
Beta strandi261 – 2633
Beta strandi265 – 2673
Beta strandi280 – 2845
Helixi288 – 29912
Beta strandi303 – 3075
Beta strandi309 – 3146
Beta strandi319 – 3224
Beta strandi325 – 3306
Beta strandi333 – 3353
Helixi341 – 3499
Beta strandi353 – 3553
Beta strandi362 – 3665
Beta strandi367 – 3693
Helixi372 – 39322
Turni394 – 3963
Beta strandi400 – 4056
Helixi408 – 45649
Turni457 – 4615
Helixi476 – 48712
Turni488 – 4903
Helixi491 – 4977
Helixi499 – 51113
Beta strandi518 – 5214
Helixi523 – 53917
Helixi544 – 5463
Turni549 – 5557
Helixi556 – 5583
Beta strandi565 – 5673
Helixi573 – 5786
Turni579 – 5813
Beta strandi583 – 5853
Beta strandi588 – 5969
Beta strandi599 – 60810
Beta strandi613 – 62311
Helixi627 – 6315
Beta strandi636 – 6416
Helixi645 – 6539
Beta strandi654 – 6563
Beta strandi660 – 6656
Beta strandi676 – 6805
Beta strandi683 – 6853
Turni686 – 6894
Beta strandi690 – 6956
Beta strandi698 – 70710
Helixi710 – 7156
Helixi720 – 73516
Turni737 – 7393
Beta strandi744 – 7485
Turni751 – 7533
Turni755 – 7573
Beta strandi758 – 7603
Helixi771 – 7777
Beta strandi796 – 7983
Helixi801 – 8033
Beta strandi805 – 8073
Helixi811 – 82919
Helixi833 – 8353

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2COMNMR-A169-279[»]
2DW4X-ray2.30A172-831[»]
2EJRX-ray2.70A172-833[»]
2H94X-ray2.90A172-835[»]
2HKOX-ray2.80A172-835[»]
2IW5X-ray2.57A171-836[»]
2L3DNMR-A174-273[»]
2UXNX-ray2.72A171-836[»]
2UXXX-ray2.74A171-836[»]
2V1DX-ray3.10A123-852[»]
2X0LX-ray3.00A123-852[»]
2XAFX-ray3.25A1-852[»]
2XAGX-ray3.10A1-852[»]
2XAHX-ray3.10A1-852[»]
2XAJX-ray3.30A1-852[»]
2XAQX-ray3.20A1-852[»]
2XASX-ray3.20A1-852[»]
2Y48X-ray3.00A123-852[»]
2Z3YX-ray2.25A172-833[»]
2Z5UX-ray2.25A172-833[»]
3ABTX-ray3.20A172-833[»]
3ABUX-ray3.10A172-833[»]
3ZMSX-ray2.96A1-852[»]
3ZMTX-ray3.10A1-852[»]
3ZMUX-ray3.20A1-852[»]
3ZMVX-ray3.00A1-852[»]
3ZMZX-ray3.00A1-852[»]
3ZN0X-ray2.80A1-852[»]
3ZN1X-ray3.10A1-852[»]
4BAYX-ray3.10A172-852[»]
4CZZX-ray3.00A1-852[»]
4KUMX-ray3.05A171-836[»]
4UV8X-ray2.80A1-852[»]
4UV9X-ray3.00A1-852[»]
4UVAX-ray2.90A1-852[»]
4UVBX-ray2.80A1-852[»]
4UVCX-ray3.10A1-852[»]
ProteinModelPortaliO60341.
SMRiO60341. Positions 171-836.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO60341.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini174 – 273100SWIRMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni300 – 852553Demethylase activityAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili110 – 15142Sequence AnalysisAdd
BLAST
Coiled coili428 – 51487Sequence AnalysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi7 – 4236Ala-richAdd
BLAST
Compositional biasi152 – 1565Poly-Pro

Domaini

The SWIRM domain may act as an anchor site for a histone tail.1 Publication

Sequence similaritiesi

Belongs to the flavin monoamine oxidase family.Curated
Contains 1 SWIRM domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiCOG1231.
GeneTreeiENSGT00530000062888.
InParanoidiO60341.
KOiK11450.
OMAiHRIHSYL.
OrthoDBiEOG7X9G66.
PhylomeDBiO60341.
TreeFamiTF312972.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR002937. Amino_oxidase.
IPR017366. Hist_Lys-spec_deMease.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
[Graphical view]
PIRSFiPIRSF038051. Histone_Lys-demethylase. 1 hit.
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS50934. SWIRM. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: O60341-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MLSGKKAAAA AAAAAAAATG TEAGPGTAGG SENGSEVAAQ PAGLSGPAEV
60 70 80 90 100
GPGAVGERTP RKKEPPRASP PGGLAEPPGS AGPQAGPTVV PGSATPMETG
110 120 130 140 150
IAETPEGRRT SRRKRAKVEY REMDESLANL SEDEYYSEEE RNAKAEKEKK
160 170 180 190 200
LPPPPPQAPP EEENESEPEE PSGVEGAAFQ SRLPHDRMTS QEAACFPDII
210 220 230 240 250
SGPQQTQKVF LFIRNRTLQL WLDNPKIQLT FEATLQQLEA PYNSDTVLVH
260 270 280 290 300
RVHSYLERHG LINFGIYKRI KPLPTKKTGK VIIIGSGVSG LAAARQLQSF
310 320 330 340 350
GMDVTLLEAR DRVGGRVATF RKGNYVADLG AMVVTGLGGN PMAVVSKQVN
360 370 380 390 400
MELAKIKQKC PLYEANGQAV PKEKDEMVEQ EFNRLLEATS YLSHQLDFNV
410 420 430 440 450
LNNKPVSLGQ ALEVVIQLQE KHVKDEQIEH WKKIVKTQEE LKELLNKMVN
460 470 480 490 500
LKEKIKELHQ QYKEASEVKP PRDITAEFLV KSKHRDLTAL CKEYDELAET
510 520 530 540 550
QGKLEEKLQE LEANPPSDVY LSSRDRQILD WHFANLEFAN ATPLSTLSLK
560 570 580 590 600
HWDQDDDFEF TGSHLTVRNG YSCVPVALAE GLDIKLNTAV RQVRYTASGC
610 620 630 640 650
EVIAVNTRST SQTFIYKCDA VLCTLPLGVL KQQPPAVQFV PPLPEWKTSA
660 670 680 690 700
VQRMGFGNLN KVVLCFDRVF WDPSVNLFGH VGSTTASRGE LFLFWNLYKA
710 720 730 740 750
PILLALVAGE AAGIMENISD DVIVGRCLAI LKGIFGSSAV PQPKETVVSR
760 770 780 790 800
WRADPWARGS YSYVAAGSSG NDYDLMAQPI TPGPSIPGAP QPIPRLFFAG
810 820 830 840 850
EHTIRNYPAT VHGALLSGLR EAGRIADQFL GAMYTLPRQA TPGVPAQQSP

SM
Length:852
Mass (Da):92,903
Last modified:August 16, 2004 - v2
Checksum:iA61CEDE51E4E0C1D
GO
Isoform 2 (identifier: O60341-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     173-173: G → GQAGGLQDDSSGGYGDGQASG
     369-369: A → ADTVK

Note: No experimental confirmation available.

Show »
Length:876
Mass (Da):95,155
Checksum:i966CA72A70F68111
GO

Sequence cautioni

The sequence BAA25527.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti78 – 781P → Q in AAH40194. (PubMed:15489334)Curated
Sequence conflicti405 – 4051P → H in AAH48134. (PubMed:15489334)Curated
Sequence conflicti669 – 6691V → A in CAD38675. (PubMed:17974005)Curated
Sequence conflicti814 – 8141A → V in AAH16639. (PubMed:15489334)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei173 – 1731G → GQAGGLQDDSSGGYGDGQAS G in isoform 2. 1 PublicationVSP_011198
Alternative sequencei369 – 3691A → ADTVK in isoform 2. 1 PublicationVSP_011199

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB011173 mRNA. Translation: BAA25527.1. Different initiation.
AL031428 Genomic DNA. Translation: CAI19707.2.
AL031428 Genomic DNA. Translation: CAI19708.2.
BC016639 mRNA. Translation: AAH16639.1.
BC025362 mRNA. Translation: AAH25362.1.
BC040194 mRNA. Translation: AAH40194.3.
BC048134 mRNA. Translation: AAH48134.2.
AL833812 mRNA. Translation: CAD38675.2.
CCDSiCCDS30627.1. [O60341-1]
CCDS53278.1. [O60341-2]
RefSeqiNP_001009999.1. NM_001009999.2. [O60341-2]
NP_055828.2. NM_015013.3. [O60341-1]
UniGeneiHs.591518.

Genome annotation databases

EnsembliENST00000356634; ENSP00000349049; ENSG00000004487. [O60341-1]
ENST00000400181; ENSP00000383042; ENSG00000004487. [O60341-2]
GeneIDi23028.
KEGGihsa:23028.
UCSCiuc001bgi.2. human. [O60341-1]
uc001bgj.2. human. [O60341-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB011173 mRNA. Translation: BAA25527.1 . Different initiation.
AL031428 Genomic DNA. Translation: CAI19707.2 .
AL031428 Genomic DNA. Translation: CAI19708.2 .
BC016639 mRNA. Translation: AAH16639.1 .
BC025362 mRNA. Translation: AAH25362.1 .
BC040194 mRNA. Translation: AAH40194.3 .
BC048134 mRNA. Translation: AAH48134.2 .
AL833812 mRNA. Translation: CAD38675.2 .
CCDSi CCDS30627.1. [O60341-1 ]
CCDS53278.1. [O60341-2 ]
RefSeqi NP_001009999.1. NM_001009999.2. [O60341-2 ]
NP_055828.2. NM_015013.3. [O60341-1 ]
UniGenei Hs.591518.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2COM NMR - A 169-279 [» ]
2DW4 X-ray 2.30 A 172-831 [» ]
2EJR X-ray 2.70 A 172-833 [» ]
2H94 X-ray 2.90 A 172-835 [» ]
2HKO X-ray 2.80 A 172-835 [» ]
2IW5 X-ray 2.57 A 171-836 [» ]
2L3D NMR - A 174-273 [» ]
2UXN X-ray 2.72 A 171-836 [» ]
2UXX X-ray 2.74 A 171-836 [» ]
2V1D X-ray 3.10 A 123-852 [» ]
2X0L X-ray 3.00 A 123-852 [» ]
2XAF X-ray 3.25 A 1-852 [» ]
2XAG X-ray 3.10 A 1-852 [» ]
2XAH X-ray 3.10 A 1-852 [» ]
2XAJ X-ray 3.30 A 1-852 [» ]
2XAQ X-ray 3.20 A 1-852 [» ]
2XAS X-ray 3.20 A 1-852 [» ]
2Y48 X-ray 3.00 A 123-852 [» ]
2Z3Y X-ray 2.25 A 172-833 [» ]
2Z5U X-ray 2.25 A 172-833 [» ]
3ABT X-ray 3.20 A 172-833 [» ]
3ABU X-ray 3.10 A 172-833 [» ]
3ZMS X-ray 2.96 A 1-852 [» ]
3ZMT X-ray 3.10 A 1-852 [» ]
3ZMU X-ray 3.20 A 1-852 [» ]
3ZMV X-ray 3.00 A 1-852 [» ]
3ZMZ X-ray 3.00 A 1-852 [» ]
3ZN0 X-ray 2.80 A 1-852 [» ]
3ZN1 X-ray 3.10 A 1-852 [» ]
4BAY X-ray 3.10 A 172-852 [» ]
4CZZ X-ray 3.00 A 1-852 [» ]
4KUM X-ray 3.05 A 171-836 [» ]
4UV8 X-ray 2.80 A 1-852 [» ]
4UV9 X-ray 3.00 A 1-852 [» ]
4UVA X-ray 2.90 A 1-852 [» ]
4UVB X-ray 2.80 A 1-852 [» ]
4UVC X-ray 3.10 A 1-852 [» ]
ProteinModelPortali O60341.
SMRi O60341. Positions 171-836.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 116667. 286 interactions.
DIPi DIP-34641N.
IntActi O60341. 217 interactions.
MINTi MINT-1372817.

Chemistry

BindingDBi O60341.
ChEMBLi CHEMBL3137262.
GuidetoPHARMACOLOGYi 2669.

PTM databases

PhosphoSitei O60341.

Proteomic databases

MaxQBi O60341.
PaxDbi O60341.
PRIDEi O60341.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000356634 ; ENSP00000349049 ; ENSG00000004487 . [O60341-1 ]
ENST00000400181 ; ENSP00000383042 ; ENSG00000004487 . [O60341-2 ]
GeneIDi 23028.
KEGGi hsa:23028.
UCSCi uc001bgi.2. human. [O60341-1 ]
uc001bgj.2. human. [O60341-2 ]

Organism-specific databases

CTDi 23028.
GeneCardsi GC01P023347.
HGNCi HGNC:29079. KDM1A.
HPAi CAB005884.
HPA053660.
MIMi 609132. gene.
neXtProti NX_O60341.
PharmGKBi PA165751392.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1231.
GeneTreei ENSGT00530000062888.
InParanoidi O60341.
KOi K11450.
OMAi HRIHSYL.
OrthoDBi EOG7X9G66.
PhylomeDBi O60341.
TreeFami TF312972.

Enzyme and pathway databases

Reactomei REACT_24970. Factors involved in megakaryocyte development and platelet production.

Miscellaneous databases

ChiTaRSi KDM1A. human.
EvolutionaryTracei O60341.
GenomeRNAii 23028.
NextBioi 43998.
PROi O60341.
SOURCEi Search...

Gene expression databases

Bgeei O60341.
CleanExi HS_AOF2.
ExpressionAtlasi O60341. baseline and differential.
Genevestigatori O60341.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
InterProi IPR002937. Amino_oxidase.
IPR017366. Hist_Lys-spec_deMease.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
[Graphical view ]
PIRSFi PIRSF038051. Histone_Lys-demethylase. 1 hit.
SUPFAMi SSF46689. SSF46689. 1 hit.
PROSITEi PS50934. SWIRM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."
    Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 5:31-39(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Brain, Skin and Testis.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 245-852 (ISOFORM 1).
    Tissue: Brain.
  5. "A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes."
    Hakimi M.-A., Bochar D.A., Chenoweth J., Lane W.S., Mandel G., Shiekhattar R.
    Proc. Natl. Acad. Sci. U.S.A. 99:7420-7425(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, INTERACTION WITH A HISTONE DEACETYLASE-CONTAINING COMPLEX, FUNCTION.
  6. "Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1."
    Humphrey G.W., Wang Y., Russanova V.R., Hirai T., Qin J., Nakatani Y., Howard B.H.
    J. Biol. Chem. 276:6817-6824(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH THE HDAC1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION.
  7. "A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes."
    Hakimi M.-A., Dong Y., Lane W.S., Speicher D.W., Shiekhattar R.
    J. Biol. Chem. 278:7234-7239(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH A HISTONE DEACETYLASE-CONTAINING COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Histone demethylation mediated by the nuclear amine oxidase homolog LSD1."
    Shi Y.-J., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A., Shi Y.
    Cell 119:941-953(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY, FUNCTION, COFACTOR.
  9. "Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process."
    Forneris F., Binda C., Vanoni M.A., Mattevi A., Battaglioli E.
    FEBS Lett. 579:2203-2207(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY, COFACTOR.
  10. "Regulation of LSD1 histone demethylase activity by its associated factors."
    Shi Y.-J., Matson C., Lan F., Iwase S., Baba T., Shi Y.
    Mol. Cell 19:857-864(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RCOR1 AND PHF21A.
  11. "An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation."
    Lee M.G., Wynder C., Cooch N., Shiekhattar R.
    Nature 437:432-435(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RCOR1, MUTAGENESIS OF LYS-661.
  12. "LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription."
    Metzger E., Wissmann M., Yin N., Mueller J.M., Schneider R., Peters A.H.F.M., Guenther T., Buettner R., Schuele R.
    Nature 437:436-439(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH ANDR.
  13. Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
  14. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  15. Cited for: FUNCTION.
  16. "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis."
    Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III
    J. Proteome Res. 7:1346-1351(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-166, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  17. "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
    Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
    Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  18. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-104; SER-126; SER-131; SER-166 AND SER-849, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  19. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  20. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  21. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-104; SER-131 AND SER-137, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  22. "ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1."
    Lee S.W., Cho Y.S., Na J.M., Park U.H., Kang M., Kim E.J., Um S.J.
    J. Biol. Chem. 285:18-29(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ASXL1.
  23. Cited for: FUNCTION.
  24. "Requirement of the histone demethylase LSD1 in Snai1-mediated transcriptional repression during epithelial-mesenchymal transition."
    Lin T., Ponn A., Hu X., Law B.K., Lu J.
    Oncogene 29:4896-4904(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SNAI.
  25. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131; SER-137; SER-166 AND SER-849, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  26. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  27. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131; SER-137 AND SER-166, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  28. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  29. "Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase."
    Yang M., Gocke C.B., Luo X., Borek D., Tomchick D.R., Machius M., Otwinowski Z., Yu H.
    Mol. Cell 23:377-387(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.57 ANGSTROMS) OF 171-836 IN COMPLEX WITH FAD AND RCOR1.
  30. "Crystal structure of human histone lysine-specific demethylase 1 (LSD1)."
    Chen Y., Yang Y., Wang F., Wan K., Yamane K., Zhang Y., Lei M.
    Proc. Natl. Acad. Sci. U.S.A. 103:13956-13961(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 172-835 IN COMPLEX WITH FAD, MUTAGENESIS OF ASN-535; HIS-564 AND TYR-761.
  31. Cited for: STRUCTURE BY NMR OF 166-285, DOMAIN.

Entry informationi

Entry nameiKDM1A_HUMAN
AccessioniPrimary (citable) accession number: O60341
Secondary accession number(s): A8MWP9
, Q5TH94, Q5TH95, Q86VT7, Q8IXK4, Q8NDP6, Q8TAZ3, Q96AW4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: August 16, 2004
Last modified: October 29, 2014
This is version 149 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3