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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei136 – 1361Alpha-ketoglutarateBy similarity
Metal bindingi192 – 1921Iron; catalyticPROSITE-ProRule annotation
Metal bindingi194 – 1941Iron; catalyticPROSITE-ProRule annotation
Binding sitei202 – 2021Alpha-ketoglutarateBy similarity
Binding sitei210 – 2101Alpha-ketoglutarateBy similarity
Metal bindingi238 – 2381ZincBy similarity
Metal bindingi244 – 2441ZincBy similarity
Metal bindingi280 – 2801Iron; catalyticPROSITE-ProRule annotation
Metal bindingi310 – 3101ZincBy similarity
Metal bindingi312 – 3121ZincBy similarity

GO - Molecular functioni

GO - Biological processi

  • cellular response to ionizing radiation Source: MGI
  • chromatin organization Source: Reactome
  • double-strand break repair via homologous recombination Source: MGI
  • histone H3-K9 demethylation Source: WormBase
  • 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
  • site of double-strand break Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164721552.

Chemistry

ChEMBLiCHEMBL6138.

Polymorphism and mutation databases

BioMutaiKDM4D.
DMDMi239938885.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 523523Lysine-specific demethylase 4DPRO_0000234376Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei26 – 261PolyADP-ribosyl glutamic acid1 Publication
Modified residuei27 – 271PolyADP-ribosyl glutamic acid1 Publication

Keywords - PTMi

ADP-ribosylation

Proteomic databases

PaxDbiQ6B0I6.
PRIDEiQ6B0I6.

PTM databases

iPTMnetiQ6B0I6.
PhosphoSiteiQ6B0I6.

Expressioni

Gene expression databases

BgeeiQ6B0I6.
CleanExiHS_JMJD2D.
GenevisibleiQ6B0I6. HS.

Organism-specific databases

HPAiHPA055854.

Interactioni

Protein-protein interaction databases

BioGridi120819. 7 interactions.
DIPiDIP-29606N.
IntActiQ6B0I6. 2 interactions.
STRINGi9606.ENSP00000334181.

Structurei

Secondary structure

1
523
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi19 – 213Combined sources
Turni25 – 284Combined sources
Helixi31 – 4010Combined sources
Helixi43 – 464Combined sources
Beta strandi47 – 515Combined sources
Beta strandi59 – 613Combined sources
Beta strandi70 – 734Combined sources
Beta strandi75 – 828Combined sources
Beta strandi85 – 928Combined sources
Helixi98 – 1058Combined sources
Turni108 – 1103Combined sources
Helixi118 – 12811Combined sources
Helixi129 – 1313Combined sources
Beta strandi135 – 1417Combined sources
Helixi160 – 1689Combined sources
Turni173 – 1753Combined sources
Beta strandi179 – 1835Combined sources
Beta strandi188 – 1925Combined sources
Helixi195 – 1973Combined sources
Beta strandi199 – 20810Combined sources
Beta strandi210 – 2156Combined sources
Helixi217 – 2193Combined sources
Helixi220 – 23011Combined sources
Helixi232 – 2376Combined sources
Helixi241 – 2444Combined sources
Beta strandi247 – 2493Combined sources
Helixi251 – 2566Combined sources
Beta strandi262 – 2665Combined sources
Beta strandi271 – 2744Combined sources
Beta strandi279 – 29517Combined sources
Helixi300 – 3067Combined sources
Beta strandi311 – 3144Combined sources
Helixi321 – 3288Combined sources
Helixi330 – 33910Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 11-340.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ6B0I6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini18 – 6043JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini146 – 312167JmjCPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi91 – 944Poly-Lys

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.
OMAiERINIFQ.
OrthoDBiEOG7TQV03.
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 BAA91508.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti510 – 5101H → R in AAH74739 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti355 – 3551S → R.
Corresponds to variant rs35631512 [ dbSNP | Ensembl ].
VAR_057882
Natural varianti408 – 4081R → Q.2 Publications
Corresponds to variant rs3740853 [ dbSNP | Ensembl ].
VAR_026225
Natural varianti471 – 4711A → S.
Corresponds to variant rs34366036 [ dbSNP | Ensembl ].
VAR_057883

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
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. Positions 11-340.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120819. 7 interactions.
DIPiDIP-29606N.
IntActiQ6B0I6. 2 interactions.
STRINGi9606.ENSP00000334181.

Chemistry

ChEMBLiCHEMBL6138.

PTM databases

iPTMnetiQ6B0I6.
PhosphoSiteiQ6B0I6.

Polymorphism and mutation databases

BioMutaiKDM4D.
DMDMi239938885.

Proteomic databases

PaxDbiQ6B0I6.
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.
MIMi609766. gene.
neXtProtiNX_Q6B0I6.
PharmGKBiPA164721552.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ6B0I6.
KOiK06709.
OMAiERINIFQ.
OrthoDBiEOG7TQV03.
PhylomeDBiQ6B0I6.
TreeFamiTF106449.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ6B0I6.
GeneWikiiJMJD2D.
GenomeRNAii55693.
NextBioi60511.
PROiQ6B0I6.
SOURCEiSearch...

Gene expression databases

BgeeiQ6B0I6.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-408.
    Tissue: Embryo and Teratocarcinoma.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-408.
    Tissue: Brain.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 395-523.
    Tissue: Testis.
  6. "Identification and characterization of JMJD2 family genes in silico."
    Katoh M., Katoh M.
    Int. J. Oncol. 24:1623-1628(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  7. "Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases."
    Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y.
    Cell 125:467-481(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME ACTIVITY.
  8. "Poly (ADP-ribose) glycohydrolase regulates retinoic acid receptor-mediated gene expression."
    Le May N., Iltis I., Ame J.C., Zhovmer A., Biard D., Egly J.M., Schreiber V., Coin F.
    Mol. Cell 48:785-798(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ADP-RIBOSYLATION AT GLU-26 AND GLU-27.

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: May 11, 2016
This is version 105 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.