Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331Alpha-ketoglutarate
Metal bindingi189 – 1891Iron; catalytic
Metal bindingi191 – 1911Iron; catalytic
Binding sitei199 – 1991Alpha-ketoglutarateBy similarity
Binding sitei207 – 2071Alpha-ketoglutarate
Metal bindingi235 – 2351ZincBy similarity
Metal bindingi241 – 2411ZincBy similarity
Metal bindingi277 – 2771Iron; catalytic
Metal bindingi307 – 3071ZincBy similarity
Metal bindingi309 – 3091ZincBy similarity

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

PharmGKBiPA165543440.

Chemistry

ChEMBLiCHEMBL1293226.
GuidetoPHARMACOLOGYi2679.

Polymorphism and mutation databases

BioMutaiKDM4E.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 506506Lysine-specific demethylase 4EPRO_0000395404Add
BLAST

Proteomic databases

PaxDbiB2RXH2.
PRIDEiB2RXH2.

Expressioni

Organism-specific databases

HPAiHPA051740.
HPA054225.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000397239.

Chemistry

BindingDBiB2RXH2.

Structurei

Secondary structure

1
506
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi16 – 183Combined sources
Helixi22 – 254Combined sources
Helixi28 – 3710Combined sources
Helixi40 – 423Combined sources
Beta strandi44 – 485Combined sources
Beta strandi67 – 704Combined sources
Beta strandi72 – 798Combined sources
Beta strandi82 – 898Combined sources
Helixi95 – 1039Combined sources
Turni105 – 1073Combined sources
Helixi115 – 12410Combined sources
Beta strandi127 – 1293Combined sources
Beta strandi132 – 1387Combined sources
Helixi157 – 1593Combined sources
Helixi160 – 1656Combined sources
Turni170 – 1723Combined sources
Beta strandi176 – 1805Combined sources
Beta strandi185 – 1895Combined sources
Helixi192 – 1943Combined sources
Beta strandi196 – 20510Combined sources
Beta strandi207 – 2126Combined sources
Helixi214 – 2163Combined sources
Helixi217 – 22711Combined sources
Turni229 – 2313Combined sources
Turni239 – 2424Combined sources
Beta strandi244 – 2463Combined sources
Helixi248 – 2536Combined sources
Beta strandi259 – 2635Combined sources
Beta strandi268 – 2714Combined sources
Beta strandi276 – 29217Combined sources
Helixi295 – 2973Combined sources
Helixi298 – 3036Combined sources
Helixi319 – 3257Combined sources
Helixi327 – 3293Combined sources
Helixi331 – 3344Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2W2IX-ray2.10A/B/C1-336[»]
ProteinModelPortaliB2RXH2.
SMRiB2RXH2. Positions 13-335.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB2RXH2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini15 – 5743JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini143 – 309167JmjCPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi88 – 914Poly-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.
InParanoidiB2RXH2.
KOiK06709.
OMAiWRDDIVL.
OrthoDBiEOG7TQV03.
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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti26 – 261A → T.
Corresponds to variant rs12798990 [ dbSNP | Ensembl ].
VAR_063402
Natural varianti42 – 421Q → R.
Corresponds to variant rs2257265 [ dbSNP | Ensembl ].
VAR_063403
Natural varianti113 – 1131Q → R.
Corresponds to variant rs10752685 [ dbSNP | Ensembl ].
VAR_063404
Natural varianti258 – 2581F → S.
Corresponds to variant rs16921260 [ dbSNP | Ensembl ].
VAR_063405

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2W2IX-ray2.10A/B/C1-336[»]
ProteinModelPortaliB2RXH2.
SMRiB2RXH2. Positions 13-335.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000397239.

Chemistry

BindingDBiB2RXH2.
ChEMBLiCHEMBL1293226.
GuidetoPHARMACOLOGYi2679.

Polymorphism and mutation databases

BioMutaiKDM4E.

Proteomic databases

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.
PharmGKBiPA165543440.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiB2RXH2.
KOiK06709.
OMAiWRDDIVL.
OrthoDBiEOG7TQV03.
PhylomeDBiB2RXH2.
TreeFamiTF106449.

Enzyme and pathway databases

BRENDAi1.14.11.B1. 2681.

Miscellaneous databases

EvolutionaryTraceiB2RXH2.
GenomeRNAii390245.
NextBioi103576.
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...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "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].
  3. "Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family."
    Hillringhaus L., Yue W.W., Rose N.R., Ng S.S., Gileadi C., Loenarz C., Bello S.H., Bray J.E., Schofield C.J., Oppermann U.
    J. Biol. Chem. 286:41616-41625(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-336 IN COMPLEX WITH OXOGLUTARATE AND NICKEL ION, COFACTOR, FUNCTION, SUBSTRATE SPECIFICITY.

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: May 11, 2016
This is version 61 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.