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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)DescriptionActionsGraphical viewLength
    Binding sitei289FAD2 Publications1
    Binding sitei308FAD2 Publications1
    Binding sitei310FAD2 Publications1
    Binding sitei316FAD2 Publications1
    Binding sitei801FAD2 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi281 – 309FADSequence analysisAdd BLAST29
    Nucleotide bindingi332 – 333FAD2 Publications2
    Nucleotide bindingi810 – 811FAD2 Publications2

    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 deacetylase activity Source: Reactome
    • 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
    • telomeric DNA binding Source: BHF-UCL
    • telomeric repeat-containing RNA binding Source: BHF-UCL
    • transcription factor activity, sequence-specific DNA binding 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

    BioCyciZFISH:ENSG00000004487-MONOMER.
    BRENDAi1.14.11.B1. 2681.
    1.14.11.B2. 2681.
    ReactomeiR-HSA-3214815. HDACs deacetylate histones.
    R-HSA-3214842. HDMs demethylate histones.
    R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
    R-HSA-983231. Factors involved in megakaryocyte development and platelet production.
    SABIO-RKO60341.
    SIGNORiO60341.

    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
    Proteomesi
    • UP000005640 Componenti: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:29079. KDM1A.

    Subcellular locationi

    GO - Cellular componenti

    • DNA repair complex Source: MGI
    • nuclear chromatin Source: BHF-UCL
    • nuclear chromosome, telomeric region Source: BHF-UCL
    • nucleoplasm Source: HPA
    • nucleus Source: UniProtKB
    • protein complex Source: MGI
    • transcription factor complex Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Cleft palate, psychomotor retardation, and distinctive facial features (CPRF)3 Publications
    The disease is caused by mutations affecting the gene represented in this entry.
    Disease descriptionA syndrome characterized by cleft palate, developmental delay, psychomotor retardation, and facial dysmorphic features including a prominent forehead, slightly arched eyebrows, elongated palpebral fissures, a wide nasal bridge, thin lips, and widely spaced teeth. Cleft palate is a congenital fissure of the soft and/or hard palate, due to faulty fusion.
    See also OMIM:616728
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_076366379E → K in CPRF. 1 Publication1
    Natural variantiVAR_076367556D → G in CPRF. 2 Publications1
    Natural variantiVAR_076368761Y → H in CPRF. 2 Publications1

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi535N → A: Strongly reduces demethylase activity. 1 Publication1
    Mutagenesisi564H → A: Strongly reduces demethylase activity. 1 Publication1
    Mutagenesisi661K → A: Abolishes histone demethylase activity. 1 Publication1
    Mutagenesisi761Y → A: Strongly reduces demethylase activity. 1 Publication1

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    DisGeNETi23028.
    MIMi616728. phenotype.
    OpenTargetsiENSG00000004487.
    PharmGKBiPA165751392.

    Chemistry databases

    ChEMBLiCHEMBL6136.
    GuidetoPHARMACOLOGYi2669.

    Polymorphism and mutation databases

    BioMutaiKDM1A.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000998811 – 852Lysine-specific histone demethylase 1AAdd BLAST852

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei59PhosphothreonineCombined sources1
    Modified residuei104PhosphothreonineCombined sources1
    Modified residuei126PhosphoserineCombined sources1
    Modified residuei131PhosphoserineCombined sources1
    Modified residuei135PhosphotyrosineCombined sources1
    Modified residuei137PhosphoserineCombined sources1
    Modified residuei166PhosphoserineCombined sources1
    Modified residuei611PhosphoserineCombined sources1
    Modified residuei849PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    EPDiO60341.
    MaxQBiO60341.
    PaxDbiO60341.
    PeptideAtlasiO60341.
    PRIDEiO60341.

    PTM databases

    iPTMnetiO60341.
    PhosphoSitePlusiO60341.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed.1 Publication

    Gene expression databases

    BgeeiENSG00000004487.
    CleanExiHS_AOF2.
    ExpressionAtlasiO60341. baseline and differential.
    GenevisibleiO60341. HS.

    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
    CCDC53Q9Y3C04EBI-710124,EBI-712969
    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
    RCOR1Q9UKL06EBI-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
    TRAF4Q9BUZ43EBI-710124,EBI-3650647
    ZBED1O960063EBI-710124,EBI-740037

    GO - Molecular functioni

    • androgen receptor binding Source: UniProtKB
    • enzyme binding Source: BHF-UCL
    • MRF binding Source: BHF-UCL
    • p53 binding Source: BHF-UCL
    • transcription factor binding Source: BHF-UCL

    Protein-protein interaction databases

    BioGridi116667. 310 interactors.
    DIPiDIP-34641N.
    IntActiO60341. 258 interactors.
    MINTiMINT-1372817.
    STRINGi9606.ENSP00000383042.

    Chemistry databases

    BindingDBiO60341.

    Structurei

    Secondary structure

    1852
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi173 – 180Combined sources8
    Beta strandi181 – 183Combined sources3
    Beta strandi185 – 187Combined sources3
    Helixi190 – 195Combined sources6
    Helixi197 – 200Combined sources4
    Helixi204 – 223Combined sources20
    Helixi231 – 236Combined sources6
    Turni240 – 243Combined sources4
    Helixi246 – 258Combined sources13
    Beta strandi261 – 263Combined sources3
    Beta strandi265 – 267Combined sources3
    Beta strandi280 – 284Combined sources5
    Helixi288 – 299Combined sources12
    Beta strandi303 – 307Combined sources5
    Beta strandi309 – 314Combined sources6
    Beta strandi319 – 322Combined sources4
    Beta strandi325 – 330Combined sources6
    Beta strandi333 – 335Combined sources3
    Helixi341 – 349Combined sources9
    Beta strandi353 – 355Combined sources3
    Beta strandi362 – 366Combined sources5
    Beta strandi367 – 369Combined sources3
    Helixi372 – 393Combined sources22
    Turni394 – 396Combined sources3
    Beta strandi400 – 405Combined sources6
    Helixi408 – 456Combined sources49
    Turni457 – 461Combined sources5
    Helixi476 – 487Combined sources12
    Turni488 – 490Combined sources3
    Helixi491 – 497Combined sources7
    Helixi499 – 511Combined sources13
    Beta strandi518 – 521Combined sources4
    Helixi523 – 539Combined sources17
    Helixi544 – 546Combined sources3
    Turni549 – 555Combined sources7
    Helixi556 – 558Combined sources3
    Beta strandi565 – 567Combined sources3
    Helixi573 – 578Combined sources6
    Turni579 – 581Combined sources3
    Beta strandi583 – 585Combined sources3
    Beta strandi588 – 596Combined sources9
    Beta strandi599 – 608Combined sources10
    Beta strandi613 – 623Combined sources11
    Helixi627 – 631Combined sources5
    Beta strandi636 – 641Combined sources6
    Helixi645 – 653Combined sources9
    Beta strandi654 – 656Combined sources3
    Beta strandi660 – 665Combined sources6
    Beta strandi676 – 680Combined sources5
    Beta strandi683 – 685Combined sources3
    Turni686 – 689Combined sources4
    Beta strandi690 – 695Combined sources6
    Beta strandi698 – 707Combined sources10
    Helixi710 – 715Combined sources6
    Helixi720 – 735Combined sources16
    Turni737 – 739Combined sources3
    Beta strandi744 – 748Combined sources5
    Turni751 – 753Combined sources3
    Turni755 – 757Combined sources3
    Beta strandi758 – 760Combined sources3
    Helixi771 – 777Combined sources7
    Beta strandi796 – 798Combined sources3
    Helixi801 – 803Combined sources3
    Beta strandi805 – 807Combined sources3
    Helixi811 – 829Combined sources19
    Helixi833 – 835Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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[»]
    4XBFX-ray2.80A171-836[»]
    5AFWX-ray1.60B108-119[»]
    5IT3X-ray1.40A/B183-267[»]
    5L3BX-ray3.30A1-852[»]
    5L3CX-ray3.31A1-852[»]
    5L3DX-ray2.60A1-852[»]
    5L3EX-ray2.80A123-852[»]
    5L3FX-ray3.50A123-852[»]
    5L3GX-ray3.10A123-852[»]
    5LBQX-ray3.30A123-852[»]
    ProteinModelPortaliO60341.
    SMRiO60341.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO60341.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini174 – 273SWIRMPROSITE-ProRule annotationAdd BLAST100

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni300 – 852Demethylase activityAdd BLAST553

    Coiled coil

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Coiled coili110 – 151Sequence analysisAdd BLAST42
    Coiled coili428 – 514Sequence analysisAdd BLAST87

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi7 – 42Ala-richAdd BLAST36
    Compositional biasi152 – 156Poly-Pro5

    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

    eggNOGiKOG0029. Eukaryota.
    KOG0685. Eukaryota.
    ENOG410XSNC. LUCA.
    GeneTreeiENSGT00530000062888.
    InParanoidiO60341.
    KOiK11450.
    OMAiPDWKQQA.
    OrthoDBiEOG091G04NO.
    PhylomeDBiO60341.
    TreeFamiTF312972.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    3.50.50.60. 2 hits.
    InterProiIPR002937. Amino_oxidase.
    IPR023753. FAD/NAD-binding_dom.
    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.
    SSF51905. SSF51905. 3 hits.
    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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti78P → Q in AAH40194 (PubMed:15489334).Curated1
    Sequence conflicti405P → H in AAH48134 (PubMed:15489334).Curated1
    Sequence conflicti669V → A in CAD38675 (PubMed:17974005).Curated1
    Sequence conflicti814A → V in AAH16639 (PubMed:15489334).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_076366379E → K in CPRF. 1 Publication1
    Natural variantiVAR_076367556D → G in CPRF. 2 Publications1
    Natural variantiVAR_076368761Y → H in CPRF. 2 Publications1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_011198173G → GQAGGLQDDSSGGYGDGQAS G in isoform 2. 1 Publication1
    Alternative sequenceiVSP_011199369A → ADTVK in isoform 2. 1 Publication1

    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.3. human. [O60341-1]

    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
    PDB 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[»]
    4XBFX-ray2.80A171-836[»]
    5AFWX-ray1.60B108-119[»]
    5IT3X-ray1.40A/B183-267[»]
    5L3BX-ray3.30A1-852[»]
    5L3CX-ray3.31A1-852[»]
    5L3DX-ray2.60A1-852[»]
    5L3EX-ray2.80A123-852[»]
    5L3FX-ray3.50A123-852[»]
    5L3GX-ray3.10A123-852[»]
    5LBQX-ray3.30A123-852[»]
    ProteinModelPortaliO60341.
    SMRiO60341.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi116667. 310 interactors.
    DIPiDIP-34641N.
    IntActiO60341. 258 interactors.
    MINTiMINT-1372817.
    STRINGi9606.ENSP00000383042.

    Chemistry databases

    BindingDBiO60341.
    ChEMBLiCHEMBL6136.
    GuidetoPHARMACOLOGYi2669.

    PTM databases

    iPTMnetiO60341.
    PhosphoSitePlusiO60341.

    Polymorphism and mutation databases

    BioMutaiKDM1A.

    Proteomic databases

    EPDiO60341.
    MaxQBiO60341.
    PaxDbiO60341.
    PeptideAtlasiO60341.
    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.3. human. [O60341-1]

    Organism-specific databases

    CTDi23028.
    DisGeNETi23028.
    GeneCardsiKDM1A.
    HGNCiHGNC:29079. KDM1A.
    HPAiCAB005884.
    HPA053660.
    MIMi609132. gene.
    616728. phenotype.
    neXtProtiNX_O60341.
    OpenTargetsiENSG00000004487.
    PharmGKBiPA165751392.
    HUGEiSearch...
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiKOG0029. Eukaryota.
    KOG0685. Eukaryota.
    ENOG410XSNC. LUCA.
    GeneTreeiENSGT00530000062888.
    InParanoidiO60341.
    KOiK11450.
    OMAiPDWKQQA.
    OrthoDBiEOG091G04NO.
    PhylomeDBiO60341.
    TreeFamiTF312972.

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000004487-MONOMER.
    BRENDAi1.14.11.B1. 2681.
    1.14.11.B2. 2681.
    ReactomeiR-HSA-3214815. HDACs deacetylate histones.
    R-HSA-3214842. HDMs demethylate histones.
    R-HSA-5625886. Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3.
    R-HSA-983231. Factors involved in megakaryocyte development and platelet production.
    SABIO-RKO60341.
    SIGNORiO60341.

    Miscellaneous databases

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

    Gene expression databases

    BgeeiENSG00000004487.
    CleanExiHS_AOF2.
    ExpressionAtlasiO60341. baseline and differential.
    GenevisibleiO60341. HS.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    3.50.50.60. 2 hits.
    InterProiIPR002937. Amino_oxidase.
    IPR023753. FAD/NAD-binding_dom.
    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.
    SSF51905. SSF51905. 3 hits.
    PROSITEiPS50934. SWIRM. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    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: November 30, 2016
    This is version 172 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. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    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 one 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.