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Protein

Lysine-specific demethylase 4D

Gene

Kdm4d

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

Functioni

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate (By similarity).By similarity

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei1332-oxoglutarateBy similarity1
Metal bindingi189Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi191Iron; catalyticPROSITE-ProRule annotation1
Binding sitei1992-oxoglutarateBy similarity1
Binding sitei2072-oxoglutarateBy similarity1
Metal bindingi235ZincBy similarity1
Metal bindingi241Zinc; via tele nitrogenBy similarity1
Binding sitei2422-oxoglutarateBy similarity1
Metal bindingi277Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi307ZincBy similarity1
Metal bindingi309ZincBy similarity1

GO - Molecular functioni

  • chromatin DNA binding Source: MGI
  • damaged DNA binding Source: MGI
  • dioxygenase activity Source: UniProtKB-KW
  • histone demethylase activity Source: MGI
  • histone demethylase activity (H3-K9 specific) Source: MGI
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase
Biological processTranscription, 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 4D (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 3D
Jumonji domain-containing protein 2D
Gene namesi
Name:Kdm4d
Synonyms:Jhdm3d, Jmjd2d
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:3606484 Kdm4d

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002343771 – 510Lysine-specific demethylase 4DAdd BLAST510

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei23PolyADP-ribosyl glutamic acidBy similarity1
Modified residuei24PolyADP-ribosyl glutamic acidBy similarity1

Keywords - PTMi

ADP-ribosylation

Proteomic databases

PaxDbiQ3U2K5
PRIDEiQ3U2K5

PTM databases

PhosphoSitePlusiQ3U2K5

Expressioni

Gene expression databases

BgeeiENSMUSG00000053914
CleanExiMM_JMJD2D
ExpressionAtlasiQ3U2K5 baseline and differential
GenevisibleiQ3U2K5 MM

Interactioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000061632

Structurei

3D structure databases

ProteinModelPortaliQ3U2K5
SMRiQ3U2K5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini15 – 57JmjNPROSITE-ProRule annotationAdd BLAST43
Domaini143 – 309JmjCPROSITE-ProRule annotationAdd BLAST167

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi88 – 91Poly-Lys4

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated

Phylogenomic databases

eggNOGiKOG0958 Eukaryota
ENOG410XP0T LUCA
GeneTreeiENSGT00530000063342
HOGENOMiHOG000231125
InParanoidiQ3U2K5
KOiK06709
OMAiPSYEEFK
OrthoDBiEOG091G01FR
PhylomeDBiQ3U2K5
TreeFamiTF106449

Family and domain databases

InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR003349 JmjN
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS51183 JMJN, 1 hit

Sequencei

Sequence statusi: Complete.

Q3U2K5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTKSTCAQN PNCSIMIFRP TKEEFNDFDK YIAYMESQGA HRAGLAKVIP
60 70 80 90 100
PKEWRARQSY DNISNILIAT PLQQVVSGQA GVFTQYHKKK KGMTVGEYRE
110 120 130 140 150
LANSKKYQTP PHLDFEDLER KYWKNRLYES PIYGADVSGS LFDGKTQQWN
160 170 180 190 200
VGHLGTIQDL LEQECGIVIE GVNTPYLYFG MWKTTFAWHT EDMDLYSINY
210 220 230 240 250
LHFGQPKTWY AVPPEHGRRL ERLARELFPG SSQGCQAFLR HKVALISPTV
260 270 280 290 300
LKENGIPFGR ITQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
310 320 330 340 350
GKVASQCSCG EARVSFSMDA FVRILQPERY ELWKRGQDQA VVDHTETMVS
360 370 380 390 400
TSQELTTRRV TKAPRKTWGL KRLRLRQVSR SLLPIATVSN VPCNMQVCHT
410 420 430 440 450
SRQPSDVKGD DVQKSDSARA SPHPLSLPSS GHMSTRRCSL GRRPCELGAQ
460 470 480 490 500
ESSNGAPVKR QLPAGRDDTS PSPELQPQAV SGDLIVDSGL VNPGPQHLMT
510
ASEGGLTSDP
Length:510
Mass (Da):57,212
Last modified:May 16, 2006 - v2
Checksum:i6B57A0300BAD94C9
GO

Sequence cautioni

The sequence BAC26740 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAC26740 differs from that shown. Reason: Erroneous termination at position 209. Translated as Trp.Curated
The sequence BAE33135 differs from that shown. Reason: Frameshift at position 419.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti374R → L in BAC26740 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK030020 mRNA Translation: BAC26740.1 Sequence problems.
AK155227 mRNA Translation: BAE33135.1 Frameshift.
CT485607 Genomic DNA No translation available.
BC112372 mRNA Translation: AAI12373.1
CCDSiCCDS22822.2
RefSeqiNP_775609.2, NM_173433.2
XP_006510333.1, XM_006510270.2
XP_006510334.1, XM_006510271.2
UniGeneiMm.240457

Genome annotation databases

EnsembliENSMUST00000058796; ENSMUSP00000061632; ENSMUSG00000053914
GeneIDi244694
KEGGimmu:244694
UCSCiuc009oen.1 mouse

Similar proteinsi

Entry informationi

Entry nameiKDM4D_MOUSE
AccessioniPrimary (citable) accession number: Q3U2K5
Secondary accession number(s): A2CGB5
, B8JK34, Q2M1G7, Q8BI19
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 16, 2006
Last modified: March 28, 2018
This is version 89 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