ID A3KG93_MOUSE Unreviewed; 873 AA.
AC A3KG93;
DT 03-APR-2007, integrated into UniProtKB/TrEMBL.
DT 03-APR-2007, sequence version 1.
DT 24-JAN-2024, entry version 124.
DE RecName: Full=Lysine-specific histone demethylase {ECO:0000256|PIRNR:PIRNR038051};
DE EC=1.14.99.66 {ECO:0000256|PIRNR:PIRNR038051};
GN Name=Kdm1a {ECO:0000313|Ensembl:ENSMUSP00000101473.2,
GN ECO:0000313|MGI:MGI:1196256};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090 {ECO:0000313|Ensembl:ENSMUSP00000101473.2, ECO:0000313|Proteomes:UP000000589};
RN [1] {ECO:0000313|Ensembl:ENSMUSP00000101473.2, ECO:0000313|Proteomes:UP000000589}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J {ECO:0000313|Ensembl:ENSMUSP00000101473.2,
RC ECO:0000313|Proteomes:UP000000589};
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [2] {ECO:0007829|PubMed:21183079}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [3] {ECO:0000313|Ensembl:ENSMUSP00000101473.2}
RP IDENTIFICATION.
RC STRAIN=C57BL/6J {ECO:0000313|Ensembl:ENSMUSP00000101473.2};
RG Ensembl;
RL Submitted (JUL-2023) to UniProtKB.
CC -!- FUNCTION: Histone demethylase that can demethylate both 'Lys-4'
CC (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a
CC coactivator or a corepressor, depending on the context. Acts by
CC oxidizing the substrate by FAD to generate the corresponding imine that
CC is subsequently hydrolyzed. Acts as a corepressor by mediating
CC demethylation of H3K4me, a specific tag for epigenetic transcriptional
CC activation. Demethylates both mono- (H3K4me1) and di-methylated
CC (H3K4me2) H3K4me. May play a role in the repression of neuronal genes.
CC Alone, it is unable to demethylate H3K4me on nucleosomes and requires
CC the presence of RCOR1/CoREST to achieve such activity.
CC {ECO:0000256|PIRNR:PIRNR038051}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 A + 2 H2O + N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] = 2
CC AH2 + 2 formaldehyde + L-lysyl(4)-[histone H3]; Xref=Rhea:RHEA:60244,
CC Rhea:RHEA-COMP:15540, Rhea:RHEA-COMP:15547, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16842, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:29969, ChEBI:CHEBI:61976; EC=1.14.99.66;
CC Evidence={ECO:0000256|PIRNR:PIRNR038051};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000256|PIRNR:PIRNR038051,
CC ECO:0000256|PIRSR:PIRSR038051-1};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|PIRNR:PIRNR038051}.
CC -!- DOMAIN: The SWIRM domain may act as an anchor site for a histone tail.
CC {ECO:0000256|PIRNR:PIRNR038051}.
CC -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC {ECO:0000256|PIRNR:PIRNR038051}.
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DR RefSeq; NP_001334150.1; NM_001347221.1.
DR AlphaFoldDB; A3KG93; -.
DR SMR; A3KG93; -.
DR iPTMnet; A3KG93; -.
DR SwissPalm; A3KG93; -.
DR EPD; A3KG93; -.
DR jPOST; A3KG93; -.
DR MaxQB; A3KG93; -.
DR PeptideAtlas; A3KG93; -.
DR ProteomicsDB; 324891; -.
DR Antibodypedia; 3136; 838 antibodies from 47 providers.
DR DNASU; 99982; -.
DR Ensembl; ENSMUST00000105847.8; ENSMUSP00000101473.2; ENSMUSG00000036940.16.
DR GeneID; 99982; -.
DR AGR; MGI:1196256; -.
DR CTD; 23028; -.
DR MGI; MGI:1196256; Kdm1a.
DR VEuPathDB; HostDB:ENSMUSG00000036940; -.
DR GeneTree; ENSGT00940000157193; -.
DR OMA; SSRGEMF; -.
DR OrthoDB; 5402444at2759; -.
DR PhylomeDB; A3KG93; -.
DR BioGRID-ORCS; 99982; 19 hits in 129 CRISPR screens.
DR ChiTaRS; Kdm1a; mouse.
DR Proteomes; UP000000589; Chromosome 4.
DR Bgee; ENSMUSG00000036940; Expressed in urethra and 298 other cell types or tissues.
DR ExpressionAtlas; A3KG93; baseline and differential.
DR GO; GO:0000785; C:chromatin; IEA:Ensembl.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:Ensembl.
DR GO; GO:1990391; C:DNA repair complex; IEA:Ensembl.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0003682; F:chromatin binding; IEA:Ensembl.
DR GO; GO:0019899; F:enzyme binding; IEA:Ensembl.
DR GO; GO:0140682; F:FAD-dependent H3K4me/H3K4me3 demethylase activity; IEA:Ensembl.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:UniProtKB-UniRule.
DR GO; GO:0032454; F:histone H3K9 demethylase activity; IEA:Ensembl.
DR GO; GO:0042802; F:identical protein binding; IEA:Ensembl.
DR GO; GO:0043426; F:MRF binding; IEA:Ensembl.
DR GO; GO:0050681; F:nuclear androgen receptor binding; IEA:Ensembl.
DR GO; GO:0030374; F:nuclear receptor coactivator activity; IEA:Ensembl.
DR GO; GO:0002039; F:p53 binding; IEA:Ensembl.
DR GO; GO:0061752; F:telomeric repeat-containing RNA binding; IEA:Ensembl.
DR GO; GO:0000380; P:alternative mRNA splicing, via spliceosome; IEA:Ensembl.
DR GO; GO:0071320; P:cellular response to cAMP; IEA:Ensembl.
DR GO; GO:0071480; P:cellular response to gamma radiation; IEA:Ensembl.
DR GO; GO:0034644; P:cellular response to UV; IEA:Ensembl.
DR GO; GO:0021987; P:cerebral cortex development; IEA:Ensembl.
DR GO; GO:0140861; P:DNA repair-dependent chromatin remodeling; IEA:Ensembl.
DR GO; GO:0046098; P:guanine metabolic process; IEA:Ensembl.
DR GO; GO:0043518; P:negative regulation of DNA damage response, signal transduction by p53 class mediator; IEA:Ensembl.
DR GO; GO:1902166; P:negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IEA:Ensembl.
DR GO; GO:0042551; P:neuron maturation; IEA:Ensembl.
DR GO; GO:0045793; P:positive regulation of cell size; IEA:Ensembl.
DR GO; GO:0002052; P:positive regulation of neuroblast proliferation; IEA:Ensembl.
DR GO; GO:0010976; P:positive regulation of neuron projection development; IEA:Ensembl.
DR GO; GO:0031398; P:positive regulation of protein ubiquitination; IEA:Ensembl.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IEA:Ensembl.
DR GO; GO:0036211; P:protein modification process; IEA:Ensembl.
DR GO; GO:0090308; P:regulation of DNA methylation-dependent heterochromatin formation; IEA:Ensembl.
DR GO; GO:0010569; P:regulation of double-strand break repair via homologous recombination; IEA:Ensembl.
DR GO; GO:0032880; P:regulation of protein localization; IEA:Ensembl.
DR GO; GO:0060992; P:response to fungicide; IEA:Ensembl.
DR Gene3D; 3.90.660.10; -; 1.
DR Gene3D; 1.10.287.80; ATP synthase, gamma subunit, helix hairpin domain; 1.
DR Gene3D; 3.50.50.60; FAD/NAD(P)-binding domain; 2.
DR Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 1.
DR InterPro; IPR002937; Amino_oxidase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR017366; Hist_Lys-spec_deMease.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR007526; SWIRM.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR PANTHER; PTHR10742; FLAVIN MONOAMINE OXIDASE; 1.
DR PANTHER; PTHR10742:SF386; LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; 1.
DR Pfam; PF01593; Amino_oxidase; 1.
DR Pfam; PF04433; SWIRM; 1.
DR PIRSF; PIRSF038051; Histone_Lys-demethylase; 1.
DR SUPFAM; SSF54373; FAD-linked reductases, C-terminal domain; 1.
DR SUPFAM; SSF51905; FAD/NAD(P)-binding domain; 1.
DR SUPFAM; SSF46689; Homeodomain-like; 1.
DR PROSITE; PS50934; SWIRM; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator {ECO:0000256|PIRNR:PIRNR038051};
KW Coiled coil {ECO:0000256|SAM:Coils};
KW FAD {ECO:0000256|ARBA:ARBA00022827, ECO:0000256|PIRNR:PIRNR038051};
KW Flavoprotein {ECO:0000256|ARBA:ARBA00022630,
KW ECO:0000256|PIRNR:PIRNR038051}; Nucleus {ECO:0000256|PIRNR:PIRNR038051};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000256|PIRNR:PIRNR038051};
KW Proteomics identification {ECO:0007829|EPD:A3KG93,
KW ECO:0007829|MaxQB:A3KG93};
KW Reference proteome {ECO:0000313|Proteomes:UP000000589};
KW Repressor {ECO:0000256|PIRNR:PIRNR038051};
KW Transcription {ECO:0000256|PIRNR:PIRNR038051};
KW Transcription regulation {ECO:0000256|PIRNR:PIRNR038051}.
FT DOMAIN 195..294
FT /note="SWIRM"
FT /evidence="ECO:0000259|PROSITE:PS50934"
FT REGION 1..194
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 455..489
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 106..152
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 302..330
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
FT BINDING 331
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
FT BINDING 337
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
FT BINDING 353..354
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
FT BINDING 822
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
FT BINDING 831..832
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000256|PIRSR:PIRSR038051-1"
SQ SEQUENCE 873 AA; 94659 MW; A4B902DC13C6A986 CRC64;
MLSGKKAAAA AAAAAAAAAA GTEAGSGAAG GAENGSEVAA PPAGLTGPTD MATGAAGERT
PRKKEPPRAS PPGGLAEPPG SAGPQAGPTA GPGSATPMET GIAETPEGRR TSRRKRAKVE
YREMDESLAN LSEDEYYSEE ERNAKAEKEK KLPPPPPQAP PEEENESEPE EPSGQAGGLQ
DDSSGGYGDG QASGVEGAAF QSRLPHDRMT SQEAACFPDI ISGPQQTQKV FLFIRNRTLQ
LWLDNPKIQL TFEATLQQLE APYNSDTVLV HRVHSYLERH GLINFGIYKR IKPLPIKKTG
KVIIIGSGVS GLAAARQLQS FGMDVTLLEA RDRVGGRVAT FRKGNYVADL GAMVVTGLGG
NPMAVVSKQV NMELAKIKQK CPLYEANGQA VPKEKDEMVE QEFNRLLEAT SYLSHQLDFN
VLNNKPVSLG QALEVVIQLQ EKHVKDEQIE HWKKIVKTQE ELKELLNKMV NLKEKIKELH
QQYKEASEVK PPRDITAEFL VKSKHRDLTA LCKEYDELAE TQGKLEEKLQ ELEANPPSDV
YLSSRDRQIL DWHFANLEFA NATPLSTLSL KHWDQDDDFE FTGSHLTVRN GYSCVPVALA
EGLDIKLNTA VRQVRYTASG CEVIAVNTRS TSQTFIYKCD AVLCTLPLGV LKQQPPAVQF
VPPLPEWKTS AVQRMGFGNL NKVVLCFDRV FWDPSVNLFG HVGSTTASRG ELFLFWNLYK
APILLALVAG EAAGIMENIS DDVIVGRCLA ILKGIFGSSA VPQPKETVVS RWRADPWARG
SYSYVAAGSS GNDYDLMAQP ITPGPSIPGA PQPIPRLFFA GEHTIRNYPA TVHGALLSGL
REAGRIADQF LGAMYTLPRQ ATPGVPAQQS PSM
//