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Q9Y4C1

- KDM3A_HUMAN

UniProt

Q9Y4C1 - KDM3A_HUMAN

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Protein
Lysine-specific demethylase 3A
Gene
KDM3A, JHDM2A, JMJD1, JMJD1A, KIAA0742, TSGA
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 UCP1.1 Publication

Cofactori

Binds 1 Fe2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1120 – 11201Iron; catalytic Inferred
Metal bindingi1122 – 11221Iron; catalytic By similarity
Metal bindingi1249 – 12491Iron; catalytic By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri662 – 68726C6-type Reviewed prediction
Add
BLAST

GO - Molecular functioni

  1. androgen receptor binding Source: UniProtKB
  2. core promoter binding Source: Ensembl
  3. dioxygenase activity Source: UniProtKB-KW
  4. iron ion binding Source: UniProtKB
  5. sequence-specific DNA binding transcription factor activity Source: Ensembl
  6. transcription regulatory region sequence-specific DNA binding Source: Ensembl

GO - Biological processi

  1. androgen receptor signaling pathway Source: UniProtKB
  2. formaldehyde biosynthetic process Source: UniProtKB
  3. histone H3-K9 demethylation Source: UniProtKB
  4. histone H3-K9 dimethylation Source: Ensembl
  5. hormone-mediated signaling pathway Source: UniProtKB
  6. negative regulation of histone H3-K9 methylation Source: Ensembl
  7. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
  8. positive regulation of transcription, DNA-templated Source: UniProtKB
  9. spermatid nucleus elongation Source: Ensembl
  10. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Differentiation, Spermatogenesis, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 3A (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 2A
Jumonji domain-containing protein 1A
Gene namesi
Name:KDM3A
Synonyms:JHDM2A, JMJD1, JMJD1A, KIAA0742, TSGA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:20815. KDM3A.

Subcellular locationi

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.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1120 – 11201H → Y: Abolishes histone demethylase activity. 1 Publication

Organism-specific databases

PharmGKBiPA164721293.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 13211321Lysine-specific demethylase 3A
PRO_0000084285Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei264 – 2641Phosphoserine1 Publication
Modified residuei445 – 4451Phosphoserine1 Publication
Modified residuei895 – 8951N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9Y4C1.
PaxDbiQ9Y4C1.
PRIDEiQ9Y4C1.

PTM databases

PhosphoSiteiQ9Y4C1.

Expressioni

Gene expression databases

ArrayExpressiQ9Y4C1.
BgeeiQ9Y4C1.
CleanExiHS_JMJD1A.
GenevestigatoriQ9Y4C1.

Interactioni

Protein-protein interaction databases

BioGridi120927. 15 interactions.
IntActiQ9Y4C1. 3 interactions.
MINTiMINT-6946055.
STRINGi9606.ENSP00000323659.

Structurei

3D structure databases

ProteinModelPortaliQ9Y4C1.
SMRiQ9Y4C1. Positions 941-1280.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1058 – 1281224JmjC
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi885 – 8895LXXLL motif

Domaini

The JmjC domain and the C6-type zinc-finger are required for the demethylation activity.1 Publication
Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors By similarity.1 Publication

Sequence similaritiesi

Contains 1 JmjC domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG305537.
InParanoidiQ9Y4C1.
KOiK15601.
OMAiRRLQFNK.
OrthoDBiEOG7B5WVG.
PhylomeDBiQ9Y4C1.
TreeFamiTF324723.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Y4C1-1 [UniParc]FASTAAdd to Basket

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MVLTLGESWP VLVGRRFLSL SAADGSDGSH DSWDVERVAE WPWLSGTIRA     50
VSHTDVTKKD LKVCVEFDGE SWRKRRWIEV YSLLRRAFLV EHNLVLAERK 100
SPEISERIVQ WPAITYKPLL DKAGLGSITS VRFLGDQQRV FLSKDLLKPI 150
QDVNSLRLSL TDNQIVSKEF QALIVKHLDE SHLLKGDKNL VGSEVKIYSL 200
DPSTQWFSAT VINGNPASKT LQVNCEEIPA LKIVDPSLIH VEVVHDNLVT 250
CGNSARIGAV KRKSSENNGT LVSKQAKSCS EASPSMCPVQ SVPTTVFKEI 300
LLGCTAATPP SKDPRQQSTP QAANSPPNLG AKIPQGCHKQ SLPEEISSCL 350
NTKSEALRTK PDVCKAGLLS KSSQIGTGDL KILTEPKGSC TQPKTNTDQE 400
NRLESVPQAL TGLPKECLPT KASSKAELEI ANPPELQKHL EHAPSPSDVS 450
NAPEVKAGVN SDSPNNCSGK KVEPSALACR SQNLKESSVK VDNESCCSRS 500
NNKIQNAPSR KSVLTDPAKL KKLQQSGEAF VQDDSCVNIV AQLPKCRECR 550
LDSLRKDKEQ QKDSPVFCRF FHFRRLQFNK HGVLRVEGFL TPNKYDNEAI 600
GLWLPLTKNV VGIDLDTAKY ILANIGDHFC QMVISEKEAM STIEPHRQVA 650
WKRAVKGVRE MCDVCDTTIF NLHWVCPRCG FGVCVDCYRM KRKNCQQGAA 700
YKTFSWLKCV KSQIHEPENL MPTQIIPGKA LYDVGDIVHS VRAKWGIKAN 750
CPCSNRQFKL FSKPASKEDL KQTSLAGEKP TLGAVLQQNP SVLEPAAVGG 800
EAASKPAGSM KPACPASTSP LNWLADLTSG NVNKENKEKQ PTMPILKNEI 850
KCLPPLPPLS KSSTVLHTFN STILTPVSNN NSGFLRNLLN SSTGKTENGL 900
KNTPKILDDI FASLVQNKTT SDLSKRPQGL TIKPSILGFD TPHYWLCDNR 950
LLCLQDPNNK SNWNVFRECW KQGQPVMVSG VHHKLNSELW KPESFRKEFG 1000
EQEVDLVNCR TNEIITGATV GDFWDGFEDV PNRLKNEKEP MVLKLKDWPP 1050
GEDFRDMMPS RFDDLMANIP LPEYTRRDGK LNLASRLPNY FVRPDLGPKM 1100
YNAYGLITPE DRKYGTTNLH LDVSDAANVM VYVGIPKGQC EQEEEVLKTI 1150
QDGDSDELTI KRFIEGKEKP GALWHIYAAK DTEKIREFLK KVSEEQGQEN 1200
PADHDPIHDQ SWYLDRSLRK RLHQEYGVQG WAIVQFLGDV VFIPAGAPHQ 1250
VHNLYSCIKV AEDFVSPEHV KHCFWLTQEF RYLSQTHTNH EDKLQVKNVI 1300
YHAVKDAVAM LKASESSFGK P 1321
Length:1,321
Mass (Da):147,341
Last modified:October 5, 2010 - v4
Checksum:i9689B3279F450C8A
GO

Sequence cautioni

The sequence BAA34462.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti187 – 1871D → H in a breast cancer sample; somatic mutation. 1 Publication
VAR_035940
Natural varianti194 – 1941E → K.
Corresponds to variant rs13424350 [ dbSNP | Ensembl ].
VAR_030623
Natural varianti212 – 2121I → V.3 Publications
Corresponds to variant rs2030259 [ dbSNP | Ensembl ].
VAR_026220
Natural varianti447 – 4471S → P.1 Publication
Corresponds to variant rs34605051 [ dbSNP | Ensembl ].
VAR_055977
Natural varianti710 – 7101V → E.
Corresponds to variant rs11677451 [ dbSNP | Ensembl ].
VAR_030624

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti24 – 241D → G in CAH18459. 1 Publication
Sequence conflicti24 – 241D → G in CAH18373. 1 Publication
Sequence conflicti51 – 511V → A in CAE45820. 1 Publication
Sequence conflicti500 – 5001S → G in CAH18373. 1 Publication
Sequence conflicti698 – 6981G → GG in CAH18459. 1 Publication
Sequence conflicti729 – 7291K → KG in CAH18459. 1 Publication
Sequence conflicti767 – 7671K → R in CAH18459. 1 Publication
Sequence conflicti773 – 7731T → TQT in CAH18459. 1 Publication
Sequence conflicti980 – 9801G → R in CAE45820. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB018285 mRNA. Translation: BAA34462.2. Different initiation.
AL832150 Transcribed RNA. Translation: CAH18459.3.
BX640698 mRNA. Translation: CAE45820.1.
CR749581 mRNA. Translation: CAH18373.1.
AC068288 Genomic DNA. Translation: AAY24210.1.
CH471053 Genomic DNA. Translation: EAW99453.1.
CH471053 Genomic DNA. Translation: EAW99456.1.
CCDSiCCDS1990.1.
RefSeqiNP_001140160.1. NM_001146688.1.
NP_060903.2. NM_018433.5.
UniGeneiHs.557425.

Genome annotation databases

EnsembliENST00000312912; ENSP00000323659; ENSG00000115548.
ENST00000409064; ENSP00000386516; ENSG00000115548.
ENST00000409556; ENSP00000386660; ENSG00000115548.
GeneIDi55818.
KEGGihsa:55818.
UCSCiuc002sri.4. human.

Polymorphism databases

DMDMi308153659.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB018285 mRNA. Translation: BAA34462.2 . Different initiation.
AL832150 Transcribed RNA. Translation: CAH18459.3 .
BX640698 mRNA. Translation: CAE45820.1 .
CR749581 mRNA. Translation: CAH18373.1 .
AC068288 Genomic DNA. Translation: AAY24210.1 .
CH471053 Genomic DNA. Translation: EAW99453.1 .
CH471053 Genomic DNA. Translation: EAW99456.1 .
CCDSi CCDS1990.1.
RefSeqi NP_001140160.1. NM_001146688.1.
NP_060903.2. NM_018433.5.
UniGenei Hs.557425.

3D structure databases

ProteinModelPortali Q9Y4C1.
SMRi Q9Y4C1. Positions 941-1280.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 120927. 15 interactions.
IntActi Q9Y4C1. 3 interactions.
MINTi MINT-6946055.
STRINGi 9606.ENSP00000323659.

Chemistry

BindingDBi Q9Y4C1.
ChEMBLi CHEMBL1938209.

PTM databases

PhosphoSitei Q9Y4C1.

Polymorphism databases

DMDMi 308153659.

Proteomic databases

MaxQBi Q9Y4C1.
PaxDbi Q9Y4C1.
PRIDEi Q9Y4C1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000312912 ; ENSP00000323659 ; ENSG00000115548 .
ENST00000409064 ; ENSP00000386516 ; ENSG00000115548 .
ENST00000409556 ; ENSP00000386660 ; ENSG00000115548 .
GeneIDi 55818.
KEGGi hsa:55818.
UCSCi uc002sri.4. human.

Organism-specific databases

CTDi 55818.
GeneCardsi GC02P086667.
H-InvDB HIX0002238.
HGNCi HGNC:20815. KDM3A.
MIMi 611512. gene.
neXtProti NX_Q9Y4C1.
PharmGKBi PA164721293.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG305537.
InParanoidi Q9Y4C1.
KOi K15601.
OMAi RRLQFNK.
OrthoDBi EOG7B5WVG.
PhylomeDBi Q9Y4C1.
TreeFami TF324723.

Miscellaneous databases

ChiTaRSi KDM3A. human.
GenomeRNAii 55818.
NextBioi 61002.
PROi Q9Y4C1.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q9Y4C1.
Bgeei Q9Y4C1.
CleanExi HS_JMJD1A.
Genevestigatori Q9Y4C1.

Family and domain databases

InterProi IPR003347. JmjC_dom.
[Graphical view ]
Pfami PF02373. JmjC. 1 hit.
[Graphical view ]
SMARTi SM00558. JmjC. 1 hit.
[Graphical view ]
PROSITEi PS51184. JMJC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "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."
    Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT VAL-212.
    Tissue: Brain.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS VAL-212 AND PRO-447.
    Tissue: Fetal kidney, Salivary gland and Testis.
  3. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    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.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT VAL-212.
  5. "JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor."
    Yamane K., Toumazou C., Tsukada Y.I., Erdjument-Bromage H., Tempst P., Wong J., Zhang Y.
    Cell 125:483-495(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, MUTAGENESIS OF HIS-1120.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-895, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "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-445, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "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-264, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: VARIANT [LARGE SCALE ANALYSIS] HIS-187.

Entry informationi

Entry nameiKDM3A_HUMAN
AccessioniPrimary (citable) accession number: Q9Y4C1
Secondary accession number(s): D6W5M3
, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: October 5, 2010
Last modified: July 9, 2014
This is version 110 of the entry and version 4 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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