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Protein

Lysine-specific demethylase 3A

Gene

Kdm3a

Organism
Mus musculus (Mouse)
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 (By similarity). Involved in spermatogenesis by regulating expression of target genes such as PRM1 and TNP1 which are required for packaging and condensation of sperm chromatin (PubMed:17943087). Involved in obesity resistance through regulation of metabolic genes such as PPARA and UCP1.By similarity2 Publications

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1122Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi1124Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi1251Iron; 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

BRENDAi1.14.11.B1 3474
ReactomeiR-MMU-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, Jmjd1a, Kiaa0742
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:98847 Kdm3a

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

Disruption phenotypei

Spermatogenesis defects and adult obesity.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000842861 – 1323Lysine-specific demethylase 3AAdd BLAST1323

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei264PhosphoserineBy similarity1
Modified residuei325PhosphoserineBy similarity1
Modified residuei446PhosphoserineBy similarity1
Modified residuei895N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ6PCM1
PaxDbiQ6PCM1
PeptideAtlasiQ6PCM1
PRIDEiQ6PCM1

PTM databases

iPTMnetiQ6PCM1
PhosphoSitePlusiQ6PCM1

Expressioni

Tissue specificityi

Highly expressed in testis (at protein level). Also expressed at high levels in tissues responsive to sympathetic nerve activity such as brown adipose tissue and skeletal muscle.1 Publication

Developmental stagei

Expression increases significantly during spermatogenesis with a 70-fold increase from day 7 testis to day 30 testis. First detected in the late pachytene stage, increases in diplotene and secondary spermatocytes and reaches its highest levels in round spermatids.1 Publication

Inductioni

By beta-adrenergic stimulation (at protein level).1 Publication

Gene expression databases

BgeeiENSMUSG00000053470 Expressed in 285 organ(s), highest expression level in blood
CleanExiMM_JMJD1A
ExpressionAtlasiQ6PCM1 baseline and differential
GenevisibleiQ6PCM1 MM

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

BioGridi222501, 1 interactor
IntActiQ6PCM1, 1 interactor
STRINGi10090.ENSMUSP00000065716

Structurei

3D structure databases

ProteinModelPortaliQ6PCM1
SMRiQ6PCM1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1060 – 1283JmjCPROSITE-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.By similarity
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
InParanoidiQ6PCM1
KOiK15601
OMAiRRWIEVY
OrthoDBiEOG091G00RB
PhylomeDBiQ6PCM1
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

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q6PCM1-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MVLTLGESWP VLVGKRFLSL SAAEGNEGGQ DNWDLERVAE WPWLSGTIRA
60 70 80 90 100
VSHTDVTKKD LKVCVEFDGE SWRKRRWIDV YSLQRKAFLV EHNLVLAERK
110 120 130 140 150
SPEVPEQVIQ WPAIMYKSLL DKAGLGAITS VRFLGDQQSV FVSKDLLKPI
160 170 180 190 200
QDVNSLRLSL TDNQTVSKEF QALIVKHLDE SHLLQGDKNL VGSEVKIYSL
210 220 230 240 250
DPSTQWFSAT VVHGNPSSKT LQVNCEEIPA LKIVDPALIH VEVVHDNFVT
260 270 280 290 300
CGNSTRTGAV KRKSSENNGS SVSKQAKSCS EASPSMCPVQ SVPTTVFKEI
310 320 330 340 350
LLGCTAATPS SKDPRQQNTP QAANSPPNIG AKLPQGCHKQ NLPEELSSCL
360 370 380 390 400
NTKPEVPRTK PDVCKEGLLS SKSSQVGAGD LKILSEPKGS CIQPKTNTDQ
410 420 430 440 450
ESRLESAPQP VTGLPKECLP AKTSSKAELD IATTPELQKH LEHAASTSDD
460 470 480 490 500
LSDKPEVKAG VTSLNSCAEK KVEPSHLGSQ SQNLKETSVK VDNESCCTRS
510 520 530 540 550
SNKTQTPPAR KSVLTDPDKV RKLQQSGEAF VQDDSCVNIV AQLPKCRECR
560 570 580 590 600
LDSLRKDKDQ QKDSPVFCRF FHFRRLQFNK HGVLRVEGFL TPNKYDSEAI
610 620 630 640 650
GLWLPLTKNV VGTDLDTAKY ILANIGDHFC QMVISEKEAM STIEPHRQVA
660 670 680 690 700
WKRAVKGVRE MCDVCDTTIF NLHWVCPRCG FGVCVDCYRM KRKNCQQGAA
710 720 730 740 750
YKTFSWIRCV KSQIHEPENL MPTQIIPGKA LYDVGDIVHS VRAKWGIKAN
760 770 780 790 800
CPCSNRQFKL FSKPALKEDL KQTSLSGEKP TLGTMVQQSS PVLEPVAVCG
810 820 830 840 850
EAASKPASSV KPTCPTSTSP LNWLADLTSG NVNKENKEKQ LTMPILKNEI
860 870 880 890 900
KCLPPLPPLN KPSTVLHTFN STILTPVSNN NSGFLRNLLN SSTAKTENGL
910 920 930 940 950
KNTPKILDDI FASLVQNKTS SDSSKRPQGL TIKPSILGFD TPHYWLCDNR
960 970 980 990 1000
LLCLQDPNNK SNWNVFRECW KQGQPVMVSG VHHKLNTELW KPESFRKEFG
1010 1020 1030 1040 1050
EQEVDLVNCR TNEIITGATV GDFWDGFEDV PNRLKNDKEK EPMVLKLKDW
1060 1070 1080 1090 1100
PPGEDFRDMM PSRFDDLMAN IPLPEYTRRD GKLNLASRLP NYFVRPDLGP
1110 1120 1130 1140 1150
KMYNAYGLIT PEDRKYGTTN LHLDVSDAAN VMVYVGIPKG QCEQEEEVLR
1160 1170 1180 1190 1200
TIQDGDSDEL TIKRFIEGKE KPGALWHIYA AKDTEKIREF LKKVSEEQGQ
1210 1220 1230 1240 1250
DNPADHDPIH DQSWYLDRSL RKRLYQEYGV QGWAIVQFLG DVVFIPAGAP
1260 1270 1280 1290 1300
HQVHNLYSCI KVAEDFVSPE HVKHCFWLTQ EFRYLSQTHT NHEDKLQVKN
1310 1320
VIYHAVKDAV AMLKASESSL GKP
Length:1,323
Mass (Da):147,847
Last modified:July 5, 2004 - v1
Checksum:i6D9C4A7779076AED
GO
Isoform 2 (identifier: Q6PCM1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-492: Missing.
     493-507: NESCCTRSSNKTQTP → MFWGDWKNIMEGAPA

Note: No experimental confirmation available.
Show »
Length:831
Mass (Da):94,415
Checksum:i63B683DCE461B7C1
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0U1RNV6A0A0U1RNV6_MOUSE
Lysine-specific demethylase 3A
Kdm3a
834Annotation score:
A0A0U1RPI3A0A0U1RPI3_MOUSE
Lysine-specific demethylase 3A
Kdm3a
43Annotation score:

Sequence cautioni

The sequence BAC98014 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti144K → Q in ABC54567 (Ref. 4) Curated1
Sequence conflicti229P → L in ABC54567 (Ref. 4) Curated1
Sequence conflicti618A → T in ABC54567 (Ref. 4) Curated1
Sequence conflicti832V → F in AAH31200 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0182961 – 492Missing in isoform 2. 1 PublicationAdd BLAST492
Alternative sequenceiVSP_018297493 – 507NESCC…KTQTP → MFWGDWKNIMEGAPA in isoform 2. 1 PublicationAdd BLAST15

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129204 mRNA Translation: BAC98014.1 Different initiation.
BC026605 mRNA Translation: AAH26605.1
BC031158 mRNA Translation: AAH31158.1
BC031200 mRNA Translation: AAH31200.1
BC059264 mRNA Translation: AAH59264.1
AK144825 mRNA Translation: BAE26085.1
AK166797 mRNA Translation: BAE39025.1
DQ323991 mRNA Translation: ABC54567.1
CCDSiCCDS20233.1 [Q6PCM1-1]
RefSeqiNP_001033784.2, NM_001038695.3 [Q6PCM1-1]
NP_766589.1, NM_173001.3 [Q6PCM1-1]
XP_006505327.1, XM_006505264.3
UniGeneiMm.260479

Genome annotation databases

EnsembliENSMUST00000065509; ENSMUSP00000065716; ENSMUSG00000053470 [Q6PCM1-1]
ENSMUST00000167220; ENSMUSP00000128789; ENSMUSG00000053470 [Q6PCM1-1]
ENSMUST00000207023; ENSMUSP00000145959; ENSMUSG00000053470 [Q6PCM1-1]
GeneIDi104263
KEGGimmu:104263
UCSCiuc009cgy.3 mouse [Q6PCM1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129204 mRNA Translation: BAC98014.1 Different initiation.
BC026605 mRNA Translation: AAH26605.1
BC031158 mRNA Translation: AAH31158.1
BC031200 mRNA Translation: AAH31200.1
BC059264 mRNA Translation: AAH59264.1
AK144825 mRNA Translation: BAE26085.1
AK166797 mRNA Translation: BAE39025.1
DQ323991 mRNA Translation: ABC54567.1
CCDSiCCDS20233.1 [Q6PCM1-1]
RefSeqiNP_001033784.2, NM_001038695.3 [Q6PCM1-1]
NP_766589.1, NM_173001.3 [Q6PCM1-1]
XP_006505327.1, XM_006505264.3
UniGeneiMm.260479

3D structure databases

ProteinModelPortaliQ6PCM1
SMRiQ6PCM1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi222501, 1 interactor
IntActiQ6PCM1, 1 interactor
STRINGi10090.ENSMUSP00000065716

PTM databases

iPTMnetiQ6PCM1
PhosphoSitePlusiQ6PCM1

Proteomic databases

EPDiQ6PCM1
PaxDbiQ6PCM1
PeptideAtlasiQ6PCM1
PRIDEiQ6PCM1

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000065509; ENSMUSP00000065716; ENSMUSG00000053470 [Q6PCM1-1]
ENSMUST00000167220; ENSMUSP00000128789; ENSMUSG00000053470 [Q6PCM1-1]
ENSMUST00000207023; ENSMUSP00000145959; ENSMUSG00000053470 [Q6PCM1-1]
GeneIDi104263
KEGGimmu:104263
UCSCiuc009cgy.3 mouse [Q6PCM1-1]

Organism-specific databases

CTDi55818
MGIiMGI:98847 Kdm3a
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1356 Eukaryota
ENOG410XTAA LUCA
GeneTreeiENSGT00530000063039
InParanoidiQ6PCM1
KOiK15601
OMAiRRWIEVY
OrthoDBiEOG091G00RB
PhylomeDBiQ6PCM1
TreeFamiTF324723

Enzyme and pathway databases

BRENDAi1.14.11.B1 3474
ReactomeiR-MMU-3214842 HDMs demethylate histones

Miscellaneous databases

ChiTaRSiKdm3a mouse
PROiPR:Q6PCM1
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000053470 Expressed in 285 organ(s), highest expression level in blood
CleanExiMM_JMJD1A
ExpressionAtlasiQ6PCM1 baseline and differential
GenevisibleiQ6PCM1 MM

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_MOUSE
AccessioniPrimary (citable) accession number: Q6PCM1
Secondary accession number(s): Q2MJQ6
, Q3TKW8, Q3UML3, Q6ZQ57, Q8K2J6, Q8K2K4, Q8R350
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: July 5, 2004
Last modified: November 7, 2018
This is version 125 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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