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Protein

Lysine-specific demethylase 4E

Gene

KDM4E

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.1 Publication

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei133Alpha-ketoglutarate1
Metal bindingi189Iron; catalytic1
Metal bindingi191Iron; catalytic1
Binding sitei199Alpha-ketoglutarateBy similarity1
Binding sitei207Alpha-ketoglutarate1
Metal bindingi235ZincBy similarity1
Metal bindingi241ZincBy similarity1
Metal bindingi277Iron; catalytic1
Metal bindingi307ZincBy similarity1
Metal bindingi309ZincBy similarity1

GO - Molecular functioni

GO - Biological processi

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.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 4E (EC:1.14.11.-)
Alternative name(s):
KDM4D-like protein
Lysine-specific demethylase 4D-like
Gene namesi
Name:KDM4E
Synonyms:KDM4DL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:37098. KDM4E.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000235268.
PharmGKBiPA165543440.

Chemistry databases

ChEMBLiCHEMBL1293226.
GuidetoPHARMACOLOGYi2679.

Polymorphism and mutation databases

BioMutaiKDM4E.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003954041 – 506Lysine-specific demethylase 4EAdd BLAST506

Proteomic databases

MaxQBiB2RXH2.
PaxDbiB2RXH2.
PRIDEiB2RXH2.

PTM databases

iPTMnetiB2RXH2.
PhosphoSitePlusiB2RXH2.

Expressioni

Organism-specific databases

HPAiHPA051740.
HPA054225.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000397239.

Chemistry databases

BindingDBiB2RXH2.

Structurei

Secondary structure

1506
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi16 – 18Combined sources3
Helixi22 – 25Combined sources4
Helixi28 – 37Combined sources10
Helixi40 – 42Combined sources3
Beta strandi44 – 48Combined sources5
Beta strandi67 – 70Combined sources4
Beta strandi72 – 79Combined sources8
Beta strandi82 – 89Combined sources8
Helixi95 – 103Combined sources9
Turni105 – 107Combined sources3
Helixi115 – 124Combined sources10
Beta strandi127 – 129Combined sources3
Beta strandi132 – 138Combined sources7
Helixi157 – 159Combined sources3
Helixi160 – 165Combined sources6
Turni170 – 172Combined sources3
Beta strandi176 – 180Combined sources5
Beta strandi185 – 189Combined sources5
Helixi192 – 194Combined sources3
Beta strandi196 – 205Combined sources10
Beta strandi207 – 212Combined sources6
Helixi214 – 216Combined sources3
Helixi217 – 227Combined sources11
Turni229 – 231Combined sources3
Turni239 – 242Combined sources4
Beta strandi244 – 246Combined sources3
Helixi248 – 253Combined sources6
Beta strandi259 – 263Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi276 – 292Combined sources17
Helixi295 – 297Combined sources3
Helixi298 – 303Combined sources6
Helixi319 – 325Combined sources7
Helixi327 – 329Combined sources3
Helixi331 – 334Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2W2IX-ray2.10A/B/C1-336[»]
ProteinModelPortaliB2RXH2.
SMRiB2RXH2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB2RXH2.

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
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiB2RXH2.
KOiK06709.
OMAiWRDDIVL.
OrthoDBiEOG091G01FR.
PhylomeDBiB2RXH2.
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.

B2RXH2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKSVHSSPQN TSHTIMTFYP TMEEFADFNT YVAYMESQGA HQAGLAKVIP
60 70 80 90 100
PKEWKARQMY DDIEDILIAT PLQQVTSGQG GVFTQYHKKK KAMRVGQYRR
110 120 130 140 150
LANSKKYQTP PHQNFADLEQ RYWKSHPGNP PIYGADISGS LFEESTKQWN
160 170 180 190 200
LGHLGTILDL LEQECGVVIE GVNTPYLYFG MWKTTFAWHT EDMDLYSINY
210 220 230 240 250
LHFGEPKTWY VVPPEHGQHL ERLARELFPD ISRGCEAFLR HKVALISPTV
260 270 280 290 300
LKENGIPFNC MTQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
310 320 330 340 350
GKMASQCSCG ESTVTFSMDP FVRIVQPESY ELWKHRQDLA IVEHTEPRVA
360 370 380 390 400
ESQELSNWRD DIVLRRAALG LRLLPNLTAQ CPTQPVSSGH CYNPKGCGTD
410 420 430 440 450
AVPGSAFQSS AYHTQTQSLT LGMSARVLLP STGSWGSGRG RGRGQGQGRG
460 470 480 490 500
CSRGRGHGCC TRELGTEEPT VQPASKRRLL MGTRSRAQGH RPQLPLANDL

MTNLSL
Length:506
Mass (Da):56,804
Last modified:July 1, 2008 - v1
Checksum:i546D69F3A159E68B
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06340226A → T.Corresponds to variant rs12798990dbSNPEnsembl.1
Natural variantiVAR_06340342Q → R.Corresponds to variant rs2257265dbSNPEnsembl.1
Natural variantiVAR_063404113Q → R.Corresponds to variant rs10752685dbSNPEnsembl.1
Natural variantiVAR_063405258F → S.Corresponds to variant rs16921260dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP002383 Genomic DNA. No translation available.
BC157851 mRNA. Translation: AAI57852.1.
BC157889 mRNA. Translation: AAI57890.1.
BC171916 mRNA. Translation: AAI71916.1.
CCDSiCCDS44713.1.
RefSeqiNP_001155102.1. NM_001161630.1.
UniGeneiHs.714692.

Genome annotation databases

EnsembliENST00000450979; ENSP00000397239; ENSG00000235268.
GeneIDi390245.
KEGGihsa:390245.
UCSCiuc010ruf.1. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP002383 Genomic DNA. No translation available.
BC157851 mRNA. Translation: AAI57852.1.
BC157889 mRNA. Translation: AAI57890.1.
BC171916 mRNA. Translation: AAI71916.1.
CCDSiCCDS44713.1.
RefSeqiNP_001155102.1. NM_001161630.1.
UniGeneiHs.714692.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2W2IX-ray2.10A/B/C1-336[»]
ProteinModelPortaliB2RXH2.
SMRiB2RXH2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000397239.

Chemistry databases

BindingDBiB2RXH2.
ChEMBLiCHEMBL1293226.
GuidetoPHARMACOLOGYi2679.

PTM databases

iPTMnetiB2RXH2.
PhosphoSitePlusiB2RXH2.

Polymorphism and mutation databases

BioMutaiKDM4E.

Proteomic databases

MaxQBiB2RXH2.
PaxDbiB2RXH2.
PRIDEiB2RXH2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000450979; ENSP00000397239; ENSG00000235268.
GeneIDi390245.
KEGGihsa:390245.
UCSCiuc010ruf.1. human.

Organism-specific databases

CTDi390245.
GeneCardsiKDM4E.
HGNCiHGNC:37098. KDM4E.
HPAiHPA051740.
HPA054225.
MIMi616581. gene.
neXtProtiNX_B2RXH2.
OpenTargetsiENSG00000235268.
PharmGKBiPA165543440.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiB2RXH2.
KOiK06709.
OMAiWRDDIVL.
OrthoDBiEOG091G01FR.
PhylomeDBiB2RXH2.
TreeFamiTF106449.

Enzyme and pathway databases

BRENDAi1.14.11.B1. 2681.

Miscellaneous databases

EvolutionaryTraceiB2RXH2.
GenomeRNAii390245.
PROiB2RXH2.
SOURCEiSearch...

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 nameiKDM4E_HUMAN
AccessioniPrimary (citable) accession number: B2RXH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 13, 2010
Last sequence update: July 1, 2008
Last modified: November 2, 2016
This is version 65 of the entry and version 1 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

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.