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Protein

Lysine-specific demethylase 4D

Gene

KDM4D

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. 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.1 Publication

Caution

It is uncertain whether Met-1 or Met-4 is the initiator.Curated

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei1362-oxoglutarateBy similarity1
Metal bindingi192Iron; catalyticPROSITE-ProRule annotation1 Publication1
Metal bindingi194Iron; catalyticPROSITE-ProRule annotation1 Publication1
Binding sitei2022-oxoglutarateBy similarity1
Binding sitei2102-oxoglutarateBy similarity1
Metal bindingi238ZincCombined sources1
Metal bindingi244Zinc; via tele nitrogenCombined sources1
Binding sitei2452-oxoglutarateBy similarity1
Metal bindingi280Iron; catalyticPROSITE-ProRule annotation1 Publication1
Metal bindingi310ZincCombined sources1
Metal bindingi312ZincCombined sources1

GO - Molecular functioni

GO - Biological processi

  • cellular response to ionizing radiation Source: MGI
  • double-strand break repair via homologous recombination Source: MGI
  • histone H3-K9 demethylation Source: UniProtKB
  • positive regulation of chromatin binding Source: MGI
  • positive regulation of double-strand break repair via nonhomologous end joining Source: MGI
  • regulation of protein phosphorylation Source: MGI
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

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

Enzyme and pathway databases

BRENDAi1.14.11.B1 2681
ReactomeiR-HSA-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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000186280.6
HGNCiHGNC:25498 KDM4D
MIMi609766 gene
neXtProtiNX_Q6B0I6

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

Organism-specific databases

DisGeNETi55693
OpenTargetsiENSG00000186280
PharmGKBiPA164721552

Chemistry databases

ChEMBLiCHEMBL6138

Polymorphism and mutation databases

BioMutaiKDM4D
DMDMi239938885

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002343761 – 523Lysine-specific demethylase 4DAdd BLAST523

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei26PolyADP-ribosyl glutamic acid1 Publication1
Modified residuei27PolyADP-ribosyl glutamic acid1 Publication1

Keywords - PTMi

ADP-ribosylation

Proteomic databases

PaxDbiQ6B0I6
PeptideAtlasiQ6B0I6
PRIDEiQ6B0I6
ProteomicsDBi66206

PTM databases

iPTMnetiQ6B0I6
PhosphoSitePlusiQ6B0I6

Expressioni

Gene expression databases

BgeeiENSG00000186280
CleanExiHS_JMJD2D
GenevisibleiQ6B0I6 HS

Organism-specific databases

HPAiHPA055854
HPA064037

Interactioni

Protein-protein interaction databases

BioGridi120819, 7 interactors
DIPiDIP-29606N
IntActiQ6B0I6, 4 interactors
STRINGi9606.ENSP00000334181

Chemistry databases

BindingDBiQ6B0I6

Structurei

Secondary structure

1523
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi19 – 21Combined sources3
Turni25 – 28Combined sources4
Helixi31 – 40Combined sources10
Helixi43 – 46Combined sources4
Beta strandi47 – 51Combined sources5
Beta strandi59 – 61Combined sources3
Helixi66 – 68Combined sources3
Beta strandi70 – 73Combined sources4
Beta strandi75 – 82Combined sources8
Beta strandi85 – 92Combined sources8
Helixi98 – 106Combined sources9
Turni108 – 110Combined sources3
Helixi118 – 128Combined sources11
Helixi129 – 131Combined sources3
Beta strandi135 – 141Combined sources7
Helixi154 – 156Combined sources3
Helixi160 – 168Combined sources9
Turni173 – 175Combined sources3
Beta strandi179 – 183Combined sources5
Beta strandi188 – 192Combined sources5
Helixi195 – 197Combined sources3
Beta strandi199 – 208Combined sources10
Beta strandi210 – 215Combined sources6
Helixi217 – 219Combined sources3
Helixi220 – 230Combined sources11
Helixi232 – 237Combined sources6
Helixi241 – 244Combined sources4
Beta strandi247 – 249Combined sources3
Helixi251 – 256Combined sources6
Beta strandi262 – 266Combined sources5
Beta strandi271 – 274Combined sources4
Beta strandi279 – 295Combined sources17
Helixi300 – 306Combined sources7
Beta strandi312 – 315Combined sources4
Helixi321 – 328Combined sources8
Helixi330 – 340Combined sources11

3D structure databases

ProteinModelPortaliQ6B0I6
SMRiQ6B0I6
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6B0I6

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini18 – 60JmjNPROSITE-ProRule annotationAdd BLAST43
Domaini146 – 312JmjCPROSITE-ProRule annotationAdd BLAST167

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi91 – 94Poly-Lys4

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated

Phylogenomic databases

eggNOGiKOG0958 Eukaryota
ENOG410XP0T LUCA
GeneTreeiENSGT00530000063342
HOGENOMiHOG000231125
InParanoidiQ6B0I6
KOiK06709
OMAiPSYEEFK
OrthoDBiEOG091G01FR
PhylomeDBiQ6B0I6
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.

Q6B0I6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
METMKSKANC AQNPNCNIMI FHPTKEEFND FDKYIAYMES QGAHRAGLAK
60 70 80 90 100
IIPPKEWKAR ETYDNISEIL IATPLQQVAS GRAGVFTQYH KKKKAMTVGE
110 120 130 140 150
YRHLANSKKY QTPPHQNFED LERKYWKNRI YNSPIYGADI SGSLFDENTK
160 170 180 190 200
QWNLGHLGTI QDLLEKECGV VIEGVNTPYL YFGMWKTTFA WHTEDMDLYS
210 220 230 240 250
INYLHLGEPK TWYVVPPEHG QRLERLAREL FPGSSRGCGA FLRHKVALIS
260 270 280 290 300
PTVLKENGIP FNRITQEAGE FMVTFPYGYH AGFNHGFNCA EAINFATPRW
310 320 330 340 350
IDYGKMASQC SCGEARVTFS MDAFVRILQP ERYDLWKRGQ DRAVVDHMEP
360 370 380 390 400
RVPASQELST QKEVQLPRRA ALGLRQLPSH WARHSPWPMA ARSGTRCHTL
410 420 430 440 450
VCSSLPRRSA VSGTATQPRA AAVHSSKKPS STPSSTPGPS AQIIHPSNGR
460 470 480 490 500
RGRGRPPQKL RAQELTLQTP AKRPLLAGTT CTASGPEPEP LPEDGALMDK
510 520
PVPLSPGLQH PVKASGCSWA PVP
Length:523
Mass (Da):58,603
Last modified:June 16, 2009 - v3
Checksum:i5303A0846ECEBA58
GO

Sequence cautioni

The sequence BAA91508 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti510H → R in AAH74739 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_057882355S → R. Corresponds to variant dbSNP:rs35631512Ensembl.1
Natural variantiVAR_026225408R → Q2 PublicationsCorresponds to variant dbSNP:rs3740853Ensembl.1
Natural variantiVAR_057883471A → S. Corresponds to variant dbSNP:rs34366036Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001113 mRNA Translation: BAA91508.1 Different initiation.
AK056162 mRNA Translation: BAG51636.1
AP002383 Genomic DNA No translation available.
CH471065 Genomic DNA Translation: EAW66952.1
BC074739 mRNA Translation: AAH74739.1
BC119010 mRNA Translation: AAI19011.1
BC122858 mRNA Translation: AAI22859.1
AL137545 mRNA Translation: CAB70803.1
CCDSiCCDS8302.1
PIRiT46388
RefSeqiNP_060509.2, NM_018039.2
UniGeneiHs.503598

Genome annotation databases

EnsembliENST00000335080; ENSP00000334181; ENSG00000186280
ENST00000536741; ENSP00000460897; ENSG00000186280
ENST00000610872; ENSP00000482224; ENSG00000186280
GeneIDi55693
KEGGihsa:55693
UCSCiuc001pfe.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiKDM4D_HUMAN
AccessioniPrimary (citable) accession number: Q6B0I6
Secondary accession number(s): B3KPC4
, Q0VF39, Q9NT41, Q9NW76
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: June 16, 2009
Last modified: June 20, 2018
This is version 125 of the entry and version 3 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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