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Protein

Lysine-specific demethylase 7A

Gene

Kdm7a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate (By similarity).By similarity1 Publication

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei279SubstrateBy similarity1
Metal bindingi282Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi284Iron; catalyticPROSITE-ProRule annotation1
Binding sitei299SubstrateBy similarity1
Metal bindingi354Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri37 – 88PHD-typePROSITE-ProRule annotationAdd BLAST52

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase
Biological processNeurogenesis, Transcription, Transcription regulation
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 7A (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 1D
Lysine-specific demethylase 7
Gene namesi
Name:Kdm7a
Synonyms:Jhdm1d, Kdm7, Kiaa1718
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:2443388 Kdm7a

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

Nucleus

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL3038497

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002267721 – 940Lysine-specific demethylase 7AAdd BLAST940

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei604PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ3UWM4
PaxDbiQ3UWM4
PeptideAtlasiQ3UWM4
PRIDEiQ3UWM4

PTM databases

iPTMnetiQ3UWM4
PhosphoSitePlusiQ3UWM4

Expressioni

Gene expression databases

BgeeiENSMUSG00000042599 Expressed in 257 organ(s), highest expression level in blood
GenevisibleiQ3UWM4 MM

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000002305

Structurei

3D structure databases

ProteinModelPortaliQ3UWM4
SMRiQ3UWM4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini230 – 386JmjCPROSITE-ProRule annotationAdd BLAST157

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni97 – 114LinkerBy similarityAdd BLAST18

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi2 – 31Ala-richAdd BLAST30

Domaini

The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2 (By similarity).By similarity
The linker region is a critical determinant of demethylase specificity. It prevents the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3, while it favors selectivity toward H3K27me2 (By similarity).By similarity

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri37 – 88PHD-typePROSITE-ProRule annotationAdd BLAST52

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
ENOG410XQXU LUCA
GeneTreeiENSGT00550000074396
HOVERGENiHBG045631
InParanoidiQ3UWM4
KOiK11445
OMAiWIKQFDT
OrthoDBiEOG091G09DB
TreeFamiTF106480

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q3UWM4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAGAAAAVAA GAAAGAAAAA GSVSAPGRAS APPPPPPVYC VCRQPYDVNR
60 70 80 90 100
FMIECDVCKD WFHGSCVGVE EHHAVDIDLY HCPDCAALHG SSLMKKRRNW
110 120 130 140 150
HRHDYTEVDD GSKPVQAGTR AFVKELRSRV FPSADEIIVK MHGSQLTQRY
160 170 180 190 200
LEKHGFDVPI MVPKLDDLGL RLPSPAFSVM DVERYVGGDK VIDVIDVARQ
210 220 230 240 250
ADSKMTLHNY VKYFMNPDRP KVLNVISLEF SDTKMSELVE VPDIARKLSW
260 270 280 290 300
VENYWPDDSV FPKPFVQKYC LMGVQDSYTD FHIDFGGTSV WYHVLWGEKI
310 320 330 340 350
FYLIKPTNEN LALYESWSSS VTQSEVFFGD KVDKCYKCVV KQGHTLFVPT
360 370 380 390 400
GWIHAVLTSQ DCMAFGGNFL HNLNIGMQLR CYEMEKRLKT PDLFKFPFFE
410 420 430 440 450
AICWFVAKSL LETLKELKED GFQPQSYLVQ GVKALHTALK LWMKKELVSE
460 470 480 490 500
HAFEIPDNVR PGHLIKELSK VIRAIEEENG KPVKSQGIPS VCPVSRPSNE
510 520 530 540 550
ASPPYHSRRK MRKLRDHNVR TPSNLDILEL HTREVLKRLE MCPWEEDLLS
560 570 580 590 600
SKLNGKFNKH LQPSSTVPEW RAKDNDLRLL LTNGRIIKDE RQLFADRSLY
610 620 630 640 650
TADSENEEDK KPTQNANMKT EQSSGREEAE SQGSPKPLNR IFTSVRSELR
660 670 680 690 700
SRPSEYSDGS DSEDSGPDCT ALKINFATED SESSGDEKKH EITSHFKEES
710 720 730 740 750
DIVRNLLQKS QKPSRQEIPV KRECPTSTST EEEAIQGMLS MAGLHYSSCL
760 770 780 790 800
QRQIQSTDCS GEKNSLQDPS SCHGSNPEFR QLYRCNKPVE FGYHAKTEDQ
810 820 830 840 850
DLMTSSWNKQ FDRTSRFNAQ DLSRSQKHIK KESSSEINQK AQSRHCVDSN
860 870 880 890 900
SSSIQNGKYT LNPSLVSCQI SNGSLSPERP IGETSFSMPL HPTKRPASNP
910 920 930 940
PPISNQATKG KRPKKGMATA KQRLGKILKL NRNGHARFFV
Length:940
Mass (Da):106,075
Last modified:March 7, 2006 - v2
Checksum:iB14FC1F85C7A5AFE
GO

Sequence cautioni

The sequence AAI45849 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAE22876 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti372N → D in BAE22890 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK042327 mRNA Translation: BAC31226.2
AK042834 mRNA Translation: BAC31377.1
AK136209 mRNA Translation: BAE22876.1 Different initiation.
AK136238 mRNA Translation: BAE22890.1
BC007161 mRNA Translation: AAH07161.1
BC145848 mRNA Translation: AAI45849.1 Different initiation.
AK129429 mRNA Translation: BAC98239.1
CCDSiCCDS51753.1
RefSeqiNP_001028602.2, NM_001033430.4
UniGeneiMm.293175

Genome annotation databases

EnsembliENSMUST00000002305; ENSMUSP00000002305; ENSMUSG00000042599
GeneIDi338523
KEGGimmu:338523
UCSCiuc009bli.2 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK042327 mRNA Translation: BAC31226.2
AK042834 mRNA Translation: BAC31377.1
AK136209 mRNA Translation: BAE22876.1 Different initiation.
AK136238 mRNA Translation: BAE22890.1
BC007161 mRNA Translation: AAH07161.1
BC145848 mRNA Translation: AAI45849.1 Different initiation.
AK129429 mRNA Translation: BAC98239.1
CCDSiCCDS51753.1
RefSeqiNP_001028602.2, NM_001033430.4
UniGeneiMm.293175

3D structure databases

ProteinModelPortaliQ3UWM4
SMRiQ3UWM4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000002305

Chemistry databases

ChEMBLiCHEMBL3038497

PTM databases

iPTMnetiQ3UWM4
PhosphoSitePlusiQ3UWM4

Proteomic databases

MaxQBiQ3UWM4
PaxDbiQ3UWM4
PeptideAtlasiQ3UWM4
PRIDEiQ3UWM4

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000002305; ENSMUSP00000002305; ENSMUSG00000042599
GeneIDi338523
KEGGimmu:338523
UCSCiuc009bli.2 mouse

Organism-specific databases

CTDi80853
MGIiMGI:2443388 Kdm7a
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
ENOG410XQXU LUCA
GeneTreeiENSGT00550000074396
HOVERGENiHBG045631
InParanoidiQ3UWM4
KOiK11445
OMAiWIKQFDT
OrthoDBiEOG091G09DB
TreeFamiTF106480

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones

Miscellaneous databases

PROiPR:Q3UWM4
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000042599 Expressed in 257 organ(s), highest expression level in blood
GenevisibleiQ3UWM4 MM

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS01359 ZF_PHD_1, 1 hit
PS50016 ZF_PHD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiKDM7A_MOUSE
AccessioniPrimary (citable) accession number: Q3UWM4
Secondary accession number(s): A6H6E5
, Q3UWN8, Q6ZPJ5, Q8C969, Q8C9E0, Q91VX8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: March 7, 2006
Last modified: November 7, 2018
This is version 103 of the entry and version 2 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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Main funding by: National Institutes of Health

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