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Protein

Lysine-specific histone demethylase 1A

Gene

KDM1A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

FAD2 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

    • androgen receptor binding Source: UniProtKB
    • chromatin binding Source: UniProtKB
    • demethylase activity Source: BHF-UCL
    • enzyme binding Source: BHF-UCL
    • flavin adenine dinucleotide binding Source: UniProtKB
    • histone demethylase activity Source: BHF-UCL
    • histone demethylase activity (H3-dimethyl-K4 specific) Source: UniProtKB
    • histone demethylase activity (H3-K4 specific) Source: UniProtKB
    • histone demethylase activity (H3-K9 specific) Source: UniProtKB
    • ligand-dependent nuclear receptor transcription coactivator activity Source: UniProtKB
    • MRF binding Source: BHF-UCL
    • oxidoreductase activity Source: UniProtKB
    • p53 binding Source: BHF-UCL
    • sequence-specific DNA binding transcription factor activity Source: Ensembl
    • transcription factor binding Source: BHF-UCL
    • transcription regulatory region DNA binding Source: BHF-UCL

    GO - Biological processi

    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

    BRENDAi1.14.11.B1. 2681.
    1.14.11.B2. 2681.
    ReactomeiREACT_24970. Factors involved in megakaryocyte development and platelet production.
    REACT_263923. HDACs deacetylate histones.
    REACT_263961. HDMs demethylate histones.
    REACT_355391. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.

    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 Componenti: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:29079. KDM1A.

    Subcellular locationi

    GO - Cellular componenti

    • nuclear chromatin Source: BHF-UCL
    • nucleoplasm Source: HPA
    • nucleus Source: UniProtKB
    • 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.

    Polymorphism and mutation databases

    BioMutaiKDM1A.

    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 residuei59 – 591Phosphothreonine1 Publication
    Modified residuei104 – 1041Phosphothreonine2 Publications
    Modified residuei126 – 1261Phosphoserine2 Publications
    Modified residuei131 – 1311Phosphoserine8 Publications
    Modified residuei135 – 1351Phosphotyrosine1 Publication
    Modified residuei137 – 1371Phosphoserine4 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. 295 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 – 1808Combined sources
    Beta strandi181 – 1833Combined sources
    Beta strandi185 – 1873Combined sources
    Helixi190 – 1956Combined sources
    Helixi197 – 2004Combined sources
    Helixi204 – 22219Combined sources
    Helixi231 – 2377Combined sources
    Helixi242 – 2443Combined sources
    Helixi246 – 25813Combined sources
    Beta strandi261 – 2633Combined sources
    Beta strandi265 – 2673Combined sources
    Beta strandi280 – 2845Combined sources
    Helixi288 – 29912Combined sources
    Beta strandi303 – 3075Combined sources
    Beta strandi309 – 3146Combined sources
    Beta strandi319 – 3224Combined sources
    Beta strandi325 – 3306Combined sources
    Beta strandi333 – 3353Combined sources
    Helixi341 – 3499Combined sources
    Beta strandi353 – 3553Combined sources
    Beta strandi362 – 3665Combined sources
    Beta strandi367 – 3693Combined sources
    Helixi372 – 39322Combined sources
    Turni394 – 3963Combined sources
    Beta strandi400 – 4056Combined sources
    Helixi408 – 45649Combined sources
    Turni457 – 4615Combined sources
    Helixi476 – 48712Combined sources
    Turni488 – 4903Combined sources
    Helixi491 – 4977Combined sources
    Helixi499 – 51113Combined sources
    Beta strandi518 – 5214Combined sources
    Helixi523 – 53917Combined sources
    Helixi544 – 5463Combined sources
    Turni549 – 5557Combined sources
    Helixi556 – 5583Combined sources
    Beta strandi565 – 5673Combined sources
    Helixi573 – 5786Combined sources
    Turni579 – 5813Combined sources
    Beta strandi583 – 5853Combined sources
    Beta strandi588 – 5969Combined sources
    Beta strandi599 – 60810Combined sources
    Beta strandi613 – 62311Combined sources
    Helixi627 – 6315Combined sources
    Beta strandi636 – 6416Combined sources
    Helixi645 – 6539Combined sources
    Beta strandi654 – 6563Combined sources
    Beta strandi660 – 6656Combined sources
    Beta strandi676 – 6805Combined sources
    Beta strandi683 – 6853Combined sources
    Turni686 – 6894Combined sources
    Beta strandi690 – 6956Combined sources
    Beta strandi698 – 70710Combined sources
    Helixi710 – 7156Combined sources
    Helixi720 – 73516Combined sources
    Turni737 – 7393Combined sources
    Beta strandi744 – 7485Combined sources
    Turni751 – 7533Combined sources
    Turni755 – 7573Combined sources
    Beta strandi758 – 7603Combined sources
    Helixi771 – 7777Combined sources
    Beta strandi796 – 7983Combined sources
    Helixi801 – 8033Combined sources
    Beta strandi805 – 8073Combined sources
    Helixi811 – 82919Combined sources
    Helixi833 – 8353Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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[»]
    4UXNX-ray2.85A1-852[»]
    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. AlignAdd to basket

    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.Curated

    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:
    EMBLi
    GenBanki
    DDBJi
    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:
    EMBLi
    GenBanki
    DDBJi
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    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[»]
    4UXNX-ray2.85A1-852[»]
    ProteinModelPortaliO60341.
    SMRiO60341. Positions 171-836.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi116667. 295 interactions.
    DIPiDIP-34641N.
    IntActiO60341. 217 interactions.
    MINTiMINT-1372817.

    Chemistry

    BindingDBiO60341.
    ChEMBLiCHEMBL6136.
    GuidetoPHARMACOLOGYi2669.

    PTM databases

    PhosphoSiteiO60341.

    Polymorphism and mutation databases

    BioMutaiKDM1A.

    Proteomic databases

    MaxQBiO60341.
    PaxDbiO60341.
    PRIDEiO60341.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    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]

    Organism-specific databases

    CTDi23028.
    GeneCardsiGC01P023347.
    HGNCiHGNC:29079. KDM1A.
    HPAiCAB005884.
    HPA053660.
    MIMi609132. gene.
    neXtProtiNX_O60341.
    PharmGKBiPA165751392.
    HUGEiSearch...
    GenAtlasiSearch...

    Phylogenomic databases

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

    Enzyme and pathway databases

    BRENDAi1.14.11.B1. 2681.
    1.14.11.B2. 2681.
    ReactomeiREACT_24970. Factors involved in megakaryocyte development and platelet production.
    REACT_263923. HDACs deacetylate histones.
    REACT_263961. HDMs demethylate histones.
    REACT_355391. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.

    Miscellaneous databases

    ChiTaRSiKDM1A. human.
    EvolutionaryTraceiO60341.
    GenomeRNAii23028.
    NextBioi43998.
    PROiO60341.
    SOURCEiSearch...

    Gene expression databases

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

    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]
    ProtoNetiSearch...

    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-59; 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. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
      Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
      J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-126; SER-131; TYR-135 AND SER-137, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    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: May 27, 2015
    This is version 156 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.