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UniProtKB/Swiss-Prot entry Q9Y4C1


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name KDM3A_HUMAN
Primary accession number Q9Y4C1
Secondary accession numbers Q53S72 Q68D47 Q68UT9 Q6N050 Q8IY08
Integrated into Swiss-Prot on November 22, 2005
Sequence was last modified on November 22, 2005 (Sequence version 3)
Annotations were last modified on    June 16, 2009 (Entry version 62)
Name and origin of the protein
Protein name Lysine-specific demethylase 3A
Synonyms EC 1.14.11.-
JmjC domain-containing histone demethylation protein 2A
Jumonji domain-containing protein 1A
Gene name
Name: KDM3A
Synonyms: JHDM2A, JMJD1, JMJD1A, KIAA0742, TSGA
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Brain;
DOI=10.1093/dnares/5.5.277; PubMed=9872452 [NCBI, ExPASy, EBI, Israel, Japan]
Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.;
"Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.";
DNA Res. 5:277-286(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANTS ILE-212 AND PRO-447.
TISSUE=Fetal kidney, Salivary gland, and Testis;
DOI=10.1186/1471-2164-8-399; PubMed=17974005 [NCBI, ExPASy, EBI, Israel, Japan]
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Blocker H., Heubner D., Hoerlein A., Michel G., Wedler H., Kohrer K., Ottenwalder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nature03466; PubMed=15815621 [NCBI, ExPASy, EBI, Israel, Japan]
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H., Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.;
"Generation and annotation of the DNA sequences of human chromosomes 2 and 4.";
Nature 434:724-731(2005).
[4]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, AND MUTAGENESIS OF HIS-1120.
DOI=10.1016/j.cell.2006.03.027; PubMed=16603237 [NCBI, ExPASy, EBI, Israel, Japan]
Yamane K., Toumazou C., Tsukada Y.I., Erdjument-Bromage H., Tempst P., Wong J., Zhang Y.;
"JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor.";
Cell 125:483-495(2006).
[5]
VARIANT [LARGE SCALE ANALYSIS] HIS-187.
DOI=10.1126/science.1133427; PubMed=16959974 [NCBI, ExPASy, EBI, Israel, Japan]
Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V., Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E.;
"The consensus coding sequences of human breast and colorectal cancers.";
Science 314:268-274(2006).
Comments
  • FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Preferentially demethylates mono- and dimethylated H3 'Lys-9' residue, with a preference for dimethylated residue, while it has weak or no activity on trimethylated H3 'Lys-9'. Demethylation of Lys residue generates formaldehyde and succinate. Involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes, resulting in H3 'Lys-9' demethylation and transcriptional activation. Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TMP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.
  • COFACTOR: Binds 1 Fe(2+) ion per subunit.
  • SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity). Note=Nuclear in round spermatids. When spermatids start to elongate, localizes to the cytoplasm where it forms distinct foci which disappear in mature spermatozoa (By similarity).
  • DOMAIN: The JmjC domain and the C6-type zinc-finger are required for the demethylation activity.
  • DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors (By similarity).
  • SIMILARITY: Belongs to the JHDM2 histone demethylase family.
  • SIMILARITY: Contains 1 JmjC domain.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AB018285; BAA34462.2; ALT_INIT; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL832150; CAH18459.3; -; Transcribed_RNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BX640698; CAE45820.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
CR749581; CAH18373.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AC068288; AAY24210.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
IPI IPI00479545; -.
UniGene Hs.557425
3D structure databases
ModBase Q9Y4C1.
PTM databases
PhosphoSite Q9Y4C1; -.
Enzyme and pathway databases
Pathway_Interaction_DB ar_pathway; Coregulation of Androgen receptor activity.
Organism-specific databases
GeneCards GC02P086580; -.
H-InvDB HIX0002238; -.
HGNC HGNC:20815; KDM3A.
GenAtlas KDM3A.
MIM 611512; gene. [NCBI / EBI]
PharmGKB PA134942779; -.
HUGE KIAA0742.
Gene expression databases
ArrayExpress Q9Y4C1; -.
Bgee Q9Y4C1; -.
CleanEx HS_JMJD1A; -.
GermOnline ENSG00000115548; Homo sapiens.
Ontologies
GO
GO:0005634; Cellular component: nucleus (inferred from direct assay from UniProtKB).
GO:0050681; Molecular function: androgen receptor binding (inferred from direct assay from UniProtKB).
GO:0005506; Molecular function: iron ion binding (inferred from mutant phenotype from UniProtKB).
GO:0016702; Molecular function: oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (inferred from electronic annotation from UniProtKB-KW).
GO:0008270; Molecular function: zinc ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0030521; Biological process: androgen receptor signaling pathway (inferred from direct assay from UniProtKB).
GO:0046293; Biological process: formaldehyde biosynthetic process (inferred from direct assay from UniProtKB).
GO:0033169; Biological process: histone H3-K9 demethylation (inferred from direct assay from UniProtKB).
GO:0009755; Biological process: hormone-mediated signaling (inferred from direct assay from UniProtKB).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
GO:0045941; Biological process: positive regulation of transcription (inferred from mutant phenotype from UniProtKB).
GO:0006355; Biological process: regulation of transcription, DNA-dependent (inferred from electronic annotation from UniProtKB-KW).
GO:0006350; Biological process: transcription (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR013129; TF_JmjC.
IPR003347; TF_JmjC_AAH.
Graphical view of domain structure.
Pfam PF02373; JmjC; 1.
Pfam graphical view of domain structure.
SMART SM00558; JmjC; 1.
SMART graphical view of domain structure.
PROSITE PS51184; JMJC; 1.
PROSITE graphical view of domain structure (profiles).
Proteomic databases
PRIDE Q9Y4C1; -.
Genome annotation databases
Ensembl ENSG00000115548; Homo sapiens. [Contig view]
Phylogenomic databases
HOVERGEN Q9Y4C1; -.
Other
SOURCE KDM3A; Homo sapiens.
ProtoNet Q9Y4C1.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Activator; Chromatin regulator; Cytoplasm; Differentiation; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase; Polymorphism; Spermatogenesis; Transcription; Transcription regulation; Zinc; Zinc-finger.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom    To Length Description FTId
CHAIN   1   1321  1321     Lysine-specific demethylase 3A. PRO_0000084285
DOMAIN   1058   1281  224     JmjC. 
ZN_FING   662    687  26     C6-type (Potential). 
MOTIF   885    889  5     LXXLL motif. 
METAL   1120   1120        Iron; catalytic (Probable). 
METAL   1122   1122        Iron; catalytic (By similarity). 
METAL   1249   1249        Iron; catalytic (By similarity). 
VARIANT   187    187  1     D -> H (in a breast cancer sample; somatic mutation). VAR_035940 
VARIANT   194    194  1     E -> K (in dbSNP:rs13424350 [NCBI]). VAR_030623 
VARIANT   212    212  1     V -> I (in dbSNP:rs2030259 [NCBI]). VAR_026220 
VARIANT   447    447  1     S -> P (in dbSNP:rs34605051 [NCBI]). VAR_055977 
VARIANT   710    710  1     V -> E (in dbSNP:rs11677451 [NCBI]). VAR_030624 
MUTAGEN   1120   1120        H->Y: Abolishes histone demethylase activity. 
CONFLICT   24     24        D -> G (in Ref. 2; CAH18459/CAH18373). 
CONFLICT   51     51        V -> A (in Ref. 2; CAE45820). 
CONFLICT   500    500        S -> G (in Ref. 2; CAH18373). 
CONFLICT   698    698        G -> GG (in Ref. 2; CAH18459). 
CONFLICT   729    729        K -> KG (in Ref. 2; CAH18459). 
CONFLICT   767    767        K -> R (in Ref. 2; CAH18459). 
CONFLICT   773    773        T -> TQT (in Ref. 2; CAH18459). 
CONFLICT   980    980        G -> R (in Ref. 2; CAE45820). 
Sequence information
Length: 1321 AA [This is the length of the unprocessed precursor] Molecular weight: 147327 Da [This is the MW of the unprocessed precursor] CRC64: 4D2B27FF5EAD738E [This is a checksum on the sequence]
        10         20         30         40         50         60 
MVLTLGESWP VLVGRRFLSL SAADGSDGSH DSWDVERVAE WPWLSGTIRA VSHTDVTKKD 

        70         80         90        100        110        120 
LKVCVEFDGE SWRKRRWIEV YSLLRRAFLV EHNLVLAERK SPEISERIVQ WPAITYKPLL 

       130        140        150        160        170        180 
DKAGLGSITS VRFLGDQQRV FLSKDLLKPI QDVNSLRLSL TDNQIVSKEF QALIVKHLDE 

       190        200        210        220        230        240 
SHLLKGDKNL VGSEVKIYSL DPSTQWFSAT VVNGNPASKT LQVNCEEIPA LKIVDPSLIH 

       250        260        270        280        290        300 
VEVVHDNLVT CGNSARIGAV KRKSSENNGT LVSKQAKSCS EASPSMCPVQ SVPTTVFKEI 

       310        320        330        340        350        360 
LLGCTAATPP SKDPRQQSTP QAANSPPNLG AKIPQGCHKQ SLPEEISSCL NTKSEALRTK 

       370        380        390        400        410        420 
PDVCKAGLLS KSSQIGTGDL KILTEPKGSC TQPKTNTDQE NRLESVPQAL TGLPKECLPT 

       430        440        450        460        470        480 
KASSKAELEI ANPPELQKHL EHAPSPSDVS NAPEVKAGVN SDSPNNCSGK KVEPSALACR 

       490        500        510        520        530        540 
SQNLKESSVK VDNESCCSRS NNKIQNAPSR KSVLTDPAKL KKLQQSGEAF VQDDSCVNIV 

       550        560        570        580        590        600 
AQLPKCRECR LDSLRKDKEQ QKDSPVFCRF FHFRRLQFNK HGVLRVEGFL TPNKYDNEAI 

       610        620        630        640        650        660 
GLWLPLTKNV VGIDLDTAKY ILANIGDHFC QMVISEKEAM STIEPHRQVA WKRAVKGVRE 

       670        680        690        700        710        720 
MCDVCDTTIF NLHWVCPRCG FGVCVDCYRM KRKNCQQGAA YKTFSWLKCV KSQIHEPENL 

       730        740        750        760        770        780 
MPTQIIPGKA LYDVGDIVHS VRAKWGIKAN CPCSNRQFKL FSKPASKEDL KQTSLAGEKP 

       790        800        810        820        830        840 
TLGAVLQQNP SVLEPAAVGG EAASKPAGSM KPACPASTSP LNWLADLTSG NVNKENKEKQ 

       850        860        870        880        890        900 
PTMPILKNEI KCLPPLPPLS KSSTVLHTFN STILTPVSNN NSGFLRNLLN SSTGKTENGL 

       910        920        930        940        950        960 
KNTPKILDDI FASLVQNKTT SDLSKRPQGL TIKPSILGFD TPHYWLCDNR LLCLQDPNNK 

       970        980        990       1000       1010       1020 
SNWNVFRECW KQGQPVMVSG VHHKLNSELW KPESFRKEFG EQEVDLVNCR TNEIITGATV 

      1030       1040       1050       1060       1070       1080 
GDFWDGFEDV PNRLKNEKEP MVLKLKDWPP GEDFRDMMPS RFDDLMANIP LPEYTRRDGK 

      1090       1100       1110       1120       1130       1140 
LNLASRLPNY FVRPDLGPKM YNAYGLITPE DRKYGTTNLH LDVSDAANVM VYVGIPKGQC 

      1150       1160       1170       1180       1190       1200 
EQEEEVLKTI QDGDSDELTI KRFIEGKEKP GALWHIYAAK DTEKIREFLK KVSEEQGQEN 

      1210       1220       1230       1240       1250       1260 
PADHDPIHDQ SWYLDRSLRK RLHQEYGVQG WAIVQFLGDV VFIPAGAPHQ VHNLYSCIKV 

      1270       1280       1290       1300       1310       1320 
AEDFVSPEHV KHCFWLTQEF RYLSQTHTNH EDKLQVKNVI YHAVKDAVAM LKASESSFGK 


P 

Q9Y4C1 in FASTA format

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