Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9Y4C1 (KDM3A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:KDM3A
Synonyms:JHDM2A, JMJD1, JMJD1A, KIAA0742, TSGA
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1321 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (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. Ref.5

Cofactor

Binds 1 Fe2+ ion per subunit. Ref.5

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. Ref.5

Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors By similarity. Ref.5

Sequence similarities

Belongs to the JHDM2 histone demethylase family.

Contains 1 JmjC domain.

Sequence caution

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

Ontologies

Keywords
   Biological processDifferentiation
Spermatogenesis
Transcription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityPolymorphism
   DomainZinc-finger
   LigandIron
Metal-binding
Zinc
   Molecular functionActivator
Chromatin regulator
Dioxygenase
Oxidoreductase
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processandrogen receptor signaling pathway

Inferred from direct assay Ref.5. Source: UniProtKB

formaldehyde biosynthetic process

Inferred from direct assay Ref.5. Source: UniProtKB

histone H3-K9 demethylation

Inferred from direct assay Ref.5. Source: UniProtKB

histone H3-K9 dimethylation

Inferred from electronic annotation. Source: Ensembl

hormone-mediated signaling pathway

Inferred from direct assay Ref.5. Source: UniProtKB

negative regulation of histone H3-K9 methylation

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription, DNA-templated

Inferred from mutant phenotype Ref.5. Source: UniProtKB

spermatid nucleus elongation

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay Ref.5. Source: UniProtKB

   Molecular_functionandrogen receptor binding

Inferred from direct assay Ref.5. Source: UniProtKB

core promoter binding

Inferred from electronic annotation. Source: Ensembl

dioxygenase activity

Inferred from electronic annotation. Source: UniProtKB-KW

iron ion binding

Inferred from mutant phenotype Ref.5. Source: UniProtKB

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: Ensembl

transcription regulatory region sequence-specific DNA binding

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 13211321Lysine-specific demethylase 3A
PRO_0000084285

Regions

Domain1058 – 1281224JmjC
Zinc finger662 – 68726C6-type Potential
Motif885 – 8895LXXLL motif

Sites

Metal binding11201Iron; catalytic Probable
Metal binding11221Iron; catalytic By similarity
Metal binding12491Iron; catalytic By similarity

Amino acid modifications

Modified residue2641Phosphoserine Ref.9
Modified residue4451Phosphoserine Ref.8
Modified residue8951N6-acetyllysine Ref.7

Natural variations

Natural variant1871D → H in a breast cancer sample; somatic mutation. Ref.10
VAR_035940
Natural variant1941E → K.
Corresponds to variant rs13424350 [ dbSNP | Ensembl ].
VAR_030623
Natural variant2121I → V. Ref.1 Ref.2 Ref.4
Corresponds to variant rs2030259 [ dbSNP | Ensembl ].
VAR_026220
Natural variant4471S → P. Ref.2
Corresponds to variant rs34605051 [ dbSNP | Ensembl ].
VAR_055977
Natural variant7101V → E.
Corresponds to variant rs11677451 [ dbSNP | Ensembl ].
VAR_030624

Experimental info

Mutagenesis11201H → Y: Abolishes histone demethylase activity. Ref.5
Sequence conflict241D → G in CAH18459. Ref.2
Sequence conflict241D → G in CAH18373. Ref.2
Sequence conflict511V → A in CAE45820. Ref.2
Sequence conflict5001S → G in CAH18373. Ref.2
Sequence conflict6981G → GG in CAH18459. Ref.2
Sequence conflict7291K → KG in CAH18459. Ref.2
Sequence conflict7671K → R in CAH18459. Ref.2
Sequence conflict7731T → TQT in CAH18459. Ref.2
Sequence conflict9801G → R in CAE45820. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q9Y4C1 [UniParc].

Last modified October 5, 2010. Version 4.
Checksum: 9689B3279F450C8A

FASTA1,321147,341
        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 VINGNPASKT 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 

« Hide

References

« Hide 'large scale' references
[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]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
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]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
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]"The consensus coding sequences of human breast and colorectal cancers."
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. expand/collapse author list , 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.
Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT [LARGE SCALE ANALYSIS] HIS-187.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS1990.1.
RefSeqNP_001140160.1. NM_001146688.1.
NP_060903.2. NM_018433.5.
UniGeneHs.557425.

3D structure databases

ProteinModelPortalQ9Y4C1.
SMRQ9Y4C1. Positions 941-1280.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120927. 15 interactions.
IntActQ9Y4C1. 3 interactions.
MINTMINT-6946055.
STRING9606.ENSP00000323659.

Chemistry

BindingDBQ9Y4C1.
ChEMBLCHEMBL1938209.

PTM databases

PhosphoSiteQ9Y4C1.

Polymorphism databases

DMDM308153659.

Proteomic databases

MaxQBQ9Y4C1.
PaxDbQ9Y4C1.
PRIDEQ9Y4C1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000312912; ENSP00000323659; ENSG00000115548.
ENST00000409064; ENSP00000386516; ENSG00000115548.
ENST00000409556; ENSP00000386660; ENSG00000115548.
GeneID55818.
KEGGhsa:55818.
UCSCuc002sri.4. human.

Organism-specific databases

CTD55818.
GeneCardsGC02P086667.
H-InvDBHIX0002238.
HGNCHGNC:20815. KDM3A.
MIM611512. gene.
neXtProtNX_Q9Y4C1.
PharmGKBPA164721293.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG305537.
InParanoidQ9Y4C1.
KOK15601.
OMARRLQFNK.
OrthoDBEOG7B5WVG.
PhylomeDBQ9Y4C1.
TreeFamTF324723.

Gene expression databases

ArrayExpressQ9Y4C1.
BgeeQ9Y4C1.
CleanExHS_JMJD1A.
GenevestigatorQ9Y4C1.

Family and domain databases

InterProIPR003347. JmjC_dom.
[Graphical view]
PfamPF02373. JmjC. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSKDM3A. human.
GenomeRNAi55818.
NextBio61002.
PROQ9Y4C1.
SOURCESearch...

Entry information

Entry nameKDM3A_HUMAN
AccessionPrimary (citable) accession number: Q9Y4C1
Secondary accession number(s): D6W5M3 expand/collapse secondary AC list , Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08
Entry history
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 statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM