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Protein

Lysine-specific demethylase 4D

Gene

KDM4D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei136Alpha-ketoglutarateBy similarity1
Metal bindingi192Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi194Iron; catalyticPROSITE-ProRule annotation1
Binding sitei202Alpha-ketoglutarateBy similarity1
Binding sitei210Alpha-ketoglutarateBy similarity1
Metal bindingi238ZincBy similarity1
Metal bindingi244ZincBy similarity1
Metal bindingi280Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi310ZincBy similarity1
Metal bindingi312ZincBy similarity1

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: WormBase
  • negative regulation of histone H3-K9 trimethylation Source: Ensembl
  • 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
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, 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

HGNCiHGNC:25498. KDM4D.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • blood microparticle Source: UniProtKB
  • nucleoplasm Source: Reactome
  • pericentric heterochromatin Source: Ensembl
  • site of double-strand break Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

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.

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. 3 interactors.
STRINGi9606.ENSP00000334181.

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
Beta strandi70 – 73Combined sources4
Beta strandi75 – 82Combined sources8
Beta strandi85 – 92Combined sources8
Helixi98 – 105Combined sources8
Turni108 – 110Combined sources3
Helixi118 – 128Combined sources11
Helixi129 – 131Combined sources3
Beta strandi135 – 141Combined sources7
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 strandi311 – 314Combined sources4
Helixi321 – 328Combined sources8
Helixi330 – 339Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3DXTX-ray1.80A1-354[»]
3DXUX-ray2.20A11-341[»]
4D6QX-ray1.29A1-342[»]
4D6RX-ray1.40A1-342[»]
4D6SX-ray1.40A1-342[»]
4HONX-ray1.80A/B12-341[»]
4HOOX-ray2.50A/B12-341[»]
5F5AX-ray1.41A1-342[»]
5F5CX-ray1.88A1-342[»]
5FP4X-ray2.00A11-341[»]
5FP8X-ray1.98A11-341[»]
5FP9X-ray2.00A11-341[»]
5FPAX-ray1.96A11-341[»]
5FPBX-ray1.91A11-341[»]
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
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ6B0I6.
KOiK06709.
OMAiKNTKRMR.
OrthoDBiEOG091G01FR.
PhylomeDBiQ6B0I6.
TreeFamiTF106449.

Family and domain databases

InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

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.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 rs35631512dbSNPEnsembl.1
Natural variantiVAR_026225408R → Q.2 PublicationsCorresponds to variant rs3740853dbSNPEnsembl.1
Natural variantiVAR_057883471A → S.Corresponds to variant rs34366036dbSNPEnsembl.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

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3DXTX-ray1.80A1-354[»]
3DXUX-ray2.20A11-341[»]
4D6QX-ray1.29A1-342[»]
4D6RX-ray1.40A1-342[»]
4D6SX-ray1.40A1-342[»]
4HONX-ray1.80A/B12-341[»]
4HOOX-ray2.50A/B12-341[»]
5F5AX-ray1.41A1-342[»]
5F5CX-ray1.88A1-342[»]
5FP4X-ray2.00A11-341[»]
5FP8X-ray1.98A11-341[»]
5FP9X-ray2.00A11-341[»]
5FPAX-ray1.96A11-341[»]
5FPBX-ray1.91A11-341[»]
ProteinModelPortaliQ6B0I6.
SMRiQ6B0I6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120819. 7 interactors.
DIPiDIP-29606N.
IntActiQ6B0I6. 3 interactors.
STRINGi9606.ENSP00000334181.

Chemistry databases

ChEMBLiCHEMBL6138.

PTM databases

iPTMnetiQ6B0I6.
PhosphoSitePlusiQ6B0I6.

Polymorphism and mutation databases

BioMutaiKDM4D.
DMDMi239938885.

Proteomic databases

PaxDbiQ6B0I6.
PeptideAtlasiQ6B0I6.
PRIDEiQ6B0I6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi55693.
GeneCardsiKDM4D.
HGNCiHGNC:25498. KDM4D.
HPAiHPA055854.
HPA064037.
MIMi609766. gene.
neXtProtiNX_Q6B0I6.
OpenTargetsiENSG00000186280.
PharmGKBiPA164721552.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ6B0I6.
KOiK06709.
OMAiKNTKRMR.
OrthoDBiEOG091G01FR.
PhylomeDBiQ6B0I6.
TreeFamiTF106449.

Enzyme and pathway databases

BRENDAi1.14.11.B1. 2681.
ReactomeiR-HSA-3214842. HDMs demethylate histones.

Miscellaneous databases

EvolutionaryTraceiQ6B0I6.
GeneWikiiJMJD2D.
GenomeRNAii55693.
PROiQ6B0I6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000186280.
CleanExiHS_JMJD2D.
GenevisibleiQ6B0I6. HS.

Family and domain databases

InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM4D_HUMAN
AccessioniPrimary (citable) accession number: Q6B0I6
Secondary accession number(s): B3KPC4
, Q0VF39, Q9NT41, Q9NW76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: June 16, 2009
Last modified: November 30, 2016
This is version 111 of the entry and version 3 of the sequence. [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

Caution

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

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.