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Protein

Lysine-specific demethylase 3A

Gene

KDM3A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1120Iron; catalyticCurated1
Metal bindingi1122Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi1249Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri662 – 687C6-typeSequence analysisAdd BLAST26

GO - Molecular functioni

GO - Biological processi

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

Enzyme and pathway databases

ReactomeiR-HSA-3214842. HDMs demethylate histones.

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
Proteomesi
  • UP000005640 Componenti: 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).By similarity

GO - Cellular componenti

  • chromatin Source: GO_Central
  • cytoplasm Source: UniProtKB-SubCell
  • membrane Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1120H → Y: Abolishes histone demethylase activity. 1 Publication1

Organism-specific databases

DisGeNETi55818.
OpenTargetsiENSG00000115548.
PharmGKBiPA164721293.

Chemistry databases

ChEMBLiCHEMBL1938209.
GuidetoPHARMACOLOGYi2673.

Polymorphism and mutation databases

BioMutaiKDM3A.
DMDMi308153659.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000842851 – 1321Lysine-specific demethylase 3AAdd BLAST1321

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei264PhosphoserineCombined sources1
Modified residuei325PhosphoserineCombined sources1
Modified residuei445PhosphoserineCombined sources1
Modified residuei766PhosphoserineCombined sources1
Modified residuei895N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9Y4C1.
MaxQBiQ9Y4C1.
PaxDbiQ9Y4C1.
PeptideAtlasiQ9Y4C1.
PRIDEiQ9Y4C1.

PTM databases

iPTMnetiQ9Y4C1.
PhosphoSitePlusiQ9Y4C1.
SwissPalmiQ9Y4C1.

Expressioni

Gene expression databases

BgeeiENSG00000115548.
CleanExiHS_JMJD1A.
ExpressionAtlasiQ9Y4C1. baseline and differential.
GenevisibleiQ9Y4C1. HS.

Organism-specific databases

HPAiHPA055543.
HPA065162.

Interactioni

GO - Molecular functioni

  • androgen receptor binding Source: UniProtKB

Protein-protein interaction databases

BioGridi120927. 27 interactors.
DIPiDIP-53661N.
IntActiQ9Y4C1. 7 interactors.
MINTiMINT-6946055.
STRINGi9606.ENSP00000323659.

Chemistry databases

BindingDBiQ9Y4C1.

Structurei

3D structure databases

ProteinModelPortaliQ9Y4C1.
SMRiQ9Y4C1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1058 – 1281JmjCPROSITE-ProRule annotationAdd BLAST224

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi885 – 889LXXLL motif5

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

Sequence similaritiesi

Belongs to the JHDM2 histone demethylase family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri662 – 687C6-typeSequence analysisAdd BLAST26

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
GeneTreeiENSGT00530000063039.
InParanoidiQ9Y4C1.
KOiK15601.
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

« Hide

        10         20         30         40         50
MVLTLGESWP VLVGRRFLSL SAADGSDGSH DSWDVERVAE WPWLSGTIRA
60 70 80 90 100
VSHTDVTKKD LKVCVEFDGE SWRKRRWIEV YSLLRRAFLV EHNLVLAERK
110 120 130 140 150
SPEISERIVQ WPAITYKPLL DKAGLGSITS VRFLGDQQRV FLSKDLLKPI
160 170 180 190 200
QDVNSLRLSL TDNQIVSKEF QALIVKHLDE SHLLKGDKNL VGSEVKIYSL
210 220 230 240 250
DPSTQWFSAT VINGNPASKT LQVNCEEIPA LKIVDPSLIH VEVVHDNLVT
260 270 280 290 300
CGNSARIGAV KRKSSENNGT LVSKQAKSCS EASPSMCPVQ SVPTTVFKEI
310 320 330 340 350
LLGCTAATPP SKDPRQQSTP QAANSPPNLG AKIPQGCHKQ SLPEEISSCL
360 370 380 390 400
NTKSEALRTK PDVCKAGLLS KSSQIGTGDL KILTEPKGSC TQPKTNTDQE
410 420 430 440 450
NRLESVPQAL TGLPKECLPT KASSKAELEI ANPPELQKHL EHAPSPSDVS
460 470 480 490 500
NAPEVKAGVN SDSPNNCSGK KVEPSALACR SQNLKESSVK VDNESCCSRS
510 520 530 540 550
NNKIQNAPSR KSVLTDPAKL KKLQQSGEAF VQDDSCVNIV AQLPKCRECR
560 570 580 590 600
LDSLRKDKEQ QKDSPVFCRF FHFRRLQFNK HGVLRVEGFL TPNKYDNEAI
610 620 630 640 650
GLWLPLTKNV VGIDLDTAKY ILANIGDHFC QMVISEKEAM STIEPHRQVA
660 670 680 690 700
WKRAVKGVRE MCDVCDTTIF NLHWVCPRCG FGVCVDCYRM KRKNCQQGAA
710 720 730 740 750
YKTFSWLKCV KSQIHEPENL MPTQIIPGKA LYDVGDIVHS VRAKWGIKAN
760 770 780 790 800
CPCSNRQFKL FSKPASKEDL KQTSLAGEKP TLGAVLQQNP SVLEPAAVGG
810 820 830 840 850
EAASKPAGSM KPACPASTSP LNWLADLTSG NVNKENKEKQ PTMPILKNEI
860 870 880 890 900
KCLPPLPPLS KSSTVLHTFN STILTPVSNN NSGFLRNLLN SSTGKTENGL
910 920 930 940 950
KNTPKILDDI FASLVQNKTT SDLSKRPQGL TIKPSILGFD TPHYWLCDNR
960 970 980 990 1000
LLCLQDPNNK SNWNVFRECW KQGQPVMVSG VHHKLNSELW KPESFRKEFG
1010 1020 1030 1040 1050
EQEVDLVNCR TNEIITGATV GDFWDGFEDV PNRLKNEKEP MVLKLKDWPP
1060 1070 1080 1090 1100
GEDFRDMMPS RFDDLMANIP LPEYTRRDGK LNLASRLPNY FVRPDLGPKM
1110 1120 1130 1140 1150
YNAYGLITPE DRKYGTTNLH LDVSDAANVM VYVGIPKGQC EQEEEVLKTI
1160 1170 1180 1190 1200
QDGDSDELTI KRFIEGKEKP GALWHIYAAK DTEKIREFLK KVSEEQGQEN
1210 1220 1230 1240 1250
PADHDPIHDQ SWYLDRSLRK RLHQEYGVQG WAIVQFLGDV VFIPAGAPHQ
1260 1270 1280 1290 1300
VHNLYSCIKV AEDFVSPEHV KHCFWLTQEF RYLSQTHTNH EDKLQVKNVI
1310 1320
YHAVKDAVAM LKASESSFGK P
Length:1,321
Mass (Da):147,341
Last modified:October 5, 2010 - v4
Checksum:i9689B3279F450C8A
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti24D → G in CAH18459 (PubMed:17974005).Curated1
Sequence conflicti24D → G in CAH18373 (PubMed:17974005).Curated1
Sequence conflicti51V → A in CAE45820 (PubMed:17974005).Curated1
Sequence conflicti500S → G in CAH18373 (PubMed:17974005).Curated1
Sequence conflicti698G → GG in CAH18459 (PubMed:17974005).Curated1
Sequence conflicti729K → KG in CAH18459 (PubMed:17974005).Curated1
Sequence conflicti767K → R in CAH18459 (PubMed:17974005).Curated1
Sequence conflicti773T → TQT in CAH18459 (PubMed:17974005).Curated1
Sequence conflicti980G → R in CAE45820 (PubMed:17974005).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_035940187D → H in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_030623194E → K.Corresponds to variant rs13424350dbSNPEnsembl.1
Natural variantiVAR_026220212I → V.3 PublicationsCorresponds to variant rs2030259dbSNPEnsembl.1
Natural variantiVAR_055977447S → P.1 PublicationCorresponds to variant rs34605051dbSNPEnsembl.1
Natural variantiVAR_030624710V → E.Corresponds to variant rs11677451dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
XP_016859982.1. XM_017004493.1.
UniGeneiHs.557425.

Genome annotation databases

EnsembliENST00000312912; ENSP00000323659; ENSG00000115548.
ENST00000409064; ENSP00000386516; ENSG00000115548.
ENST00000409556; ENSP00000386660; ENSG00000115548.
GeneIDi55818.
KEGGihsa:55818.
UCSCiuc002sri.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
XP_016859982.1. XM_017004493.1.
UniGeneiHs.557425.

3D structure databases

ProteinModelPortaliQ9Y4C1.
SMRiQ9Y4C1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120927. 27 interactors.
DIPiDIP-53661N.
IntActiQ9Y4C1. 7 interactors.
MINTiMINT-6946055.
STRINGi9606.ENSP00000323659.

Chemistry databases

BindingDBiQ9Y4C1.
ChEMBLiCHEMBL1938209.
GuidetoPHARMACOLOGYi2673.

PTM databases

iPTMnetiQ9Y4C1.
PhosphoSitePlusiQ9Y4C1.
SwissPalmiQ9Y4C1.

Polymorphism and mutation databases

BioMutaiKDM3A.
DMDMi308153659.

Proteomic databases

EPDiQ9Y4C1.
MaxQBiQ9Y4C1.
PaxDbiQ9Y4C1.
PeptideAtlasiQ9Y4C1.
PRIDEiQ9Y4C1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000312912; ENSP00000323659; ENSG00000115548.
ENST00000409064; ENSP00000386516; ENSG00000115548.
ENST00000409556; ENSP00000386660; ENSG00000115548.
GeneIDi55818.
KEGGihsa:55818.
UCSCiuc002sri.5. human.

Organism-specific databases

CTDi55818.
DisGeNETi55818.
GeneCardsiKDM3A.
H-InvDBHIX0002238.
HGNCiHGNC:20815. KDM3A.
HPAiHPA055543.
HPA065162.
MIMi611512. gene.
neXtProtiNX_Q9Y4C1.
OpenTargetsiENSG00000115548.
PharmGKBiPA164721293.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
GeneTreeiENSGT00530000063039.
InParanoidiQ9Y4C1.
KOiK15601.
PhylomeDBiQ9Y4C1.
TreeFamiTF324723.

Enzyme and pathway databases

ReactomeiR-HSA-3214842. HDMs demethylate histones.

Miscellaneous databases

ChiTaRSiKDM3A. human.
GenomeRNAii55818.
PROiQ9Y4C1.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115548.
CleanExiHS_JMJD1A.
ExpressionAtlasiQ9Y4C1. baseline and differential.
GenevisibleiQ9Y4C1. HS.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 133 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

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.