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Protein

Lysine-specific demethylase 3A

Gene

KDM3A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 TNP1 which are required for packaging and condensation of sperm chromatin. Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.2 Publications

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1120Iron; catalytic2 Publications1
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

Keywordsi

Molecular functionActivator, Chromatin regulator, Dioxygenase, Oxidoreductase
Biological processDifferentiation, Spermatogenesis, Transcription, Transcription regulation
LigandIron, 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

EuPathDBiHostDB:ENSG00000115548.16
HGNCiHGNC:20815 KDM3A
MIMi611512 gene
neXtProtiNX_Q9Y4C1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1120H → A: Abolishes lysine-specific histone demethylase activity. 1 Publication1
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
ProteomicsDBi86157

PTM databases

CarbonylDBiQ9Y4C1
iPTMnetiQ9Y4C1
PhosphoSitePlusiQ9Y4C1
SwissPalmiQ9Y4C1

Expressioni

Gene expression databases

BgeeiENSG00000115548 Expressed in 232 organ(s), highest expression level in testis
CleanExiHS_JMJD1A
ExpressionAtlasiQ9Y4C1 baseline and differential
GenevisibleiQ9Y4C1 HS

Organism-specific databases

HPAiHPA055543
HPA065162

Interactioni

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi120927, 28 interactors
DIPiDIP-53661N
IntActiQ9Y4C1, 10 interactors
MINTiQ9Y4C1
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

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

InterProiView protein in InterPro
IPR003347 JmjC_dom
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 4 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F5H070F5H070_HUMAN
Lysine-specific demethylase 3A
KDM3A
1,327Annotation score:
C9JC73C9JC73_HUMAN
Lysine-specific demethylase 3A
KDM3A
121Annotation score:
C9J7Q7C9J7Q7_HUMAN
Lysine-specific demethylase 3A
KDM3A
170Annotation score:
F8WE62F8WE62_HUMAN
Lysine-specific demethylase 3A
KDM3A
711Annotation score:

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 dbSNP:rs13424350Ensembl.1
Natural variantiVAR_026220212I → V3 PublicationsCorresponds to variant dbSNP:rs2030259Ensembl.1
Natural variantiVAR_055977447S → P1 PublicationCorresponds to variant dbSNP:rs34605051Ensembl.1
Natural variantiVAR_030624710V → E. Corresponds to variant dbSNP:rs11677451Ensembl.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

Similar proteinsi

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, 28 interactors
DIPiDIP-53661N
IntActiQ9Y4C1, 10 interactors
MINTiQ9Y4C1
STRINGi9606.ENSP00000323659

Chemistry databases

BindingDBiQ9Y4C1
ChEMBLiCHEMBL1938209
GuidetoPHARMACOLOGYi2673

PTM databases

CarbonylDBiQ9Y4C1
iPTMnetiQ9Y4C1
PhosphoSitePlusiQ9Y4C1
SwissPalmiQ9Y4C1

Polymorphism and mutation databases

BioMutaiKDM3A
DMDMi308153659

Proteomic databases

EPDiQ9Y4C1
MaxQBiQ9Y4C1
PaxDbiQ9Y4C1
PeptideAtlasiQ9Y4C1
PRIDEiQ9Y4C1
ProteomicsDBi86157

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
EuPathDBiHostDB:ENSG00000115548.16
GeneCardsiKDM3A
H-InvDBiHIX0002238
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
PROiPR:Q9Y4C1
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115548 Expressed in 232 organ(s), highest expression level in testis
CleanExiHS_JMJD1A
ExpressionAtlasiQ9Y4C1 baseline and differential
GenevisibleiQ9Y4C1 HS

Family and domain databases

InterProiView protein in InterPro
IPR003347 JmjC_dom
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiKDM3A_HUMAN
AccessioniPrimary (citable) accession number: Q9Y4C1
Secondary accession number(s): D6W5M3
, Q53S72, Q68D47, Q68UT9, Q6N050, Q8IY08
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: October 5, 2010
Last modified: November 7, 2018
This is version 145 of the entry and version 4 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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