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Protein

Lysine-specific demethylase 4D

Gene

Kdm4d

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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 (By similarity).By similarity

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331Alpha-ketoglutarateBy similarity
Metal bindingi189 – 1891Iron; catalyticPROSITE-ProRule annotation
Metal bindingi191 – 1911Iron; catalyticPROSITE-ProRule annotation
Binding sitei199 – 1991Alpha-ketoglutarateBy similarity
Binding sitei207 – 2071Alpha-ketoglutarateBy similarity
Metal bindingi235 – 2351ZincBy similarity
Metal bindingi241 – 2411ZincBy similarity
Metal bindingi277 – 2771Iron; catalyticPROSITE-ProRule annotation
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

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
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 8

Organism-specific databases

RGDi1591045. Kdm4d.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 510510Lysine-specific demethylase 4DPRO_0000376824Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei23 – 231PolyADP-ribosyl glutamic acidBy similarity
Modified residuei24 – 241PolyADP-ribosyl glutamic acidBy similarity

Keywords - PTMi

ADP-ribosylation

Proteomic databases

PaxDbiA1A5Q5.
PRIDEiA1A5Q5.

Expressioni

Gene expression databases

BgeeiENSRNOG00000024726.
GenevisibleiA1A5Q5. RN.

Interactioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000067344.

Structurei

3D structure databases

ProteinModelPortaliA1A5Q5.
SMRiA1A5Q5. Positions 10-345.
ModBaseiSearch...
MobiDBiSearch...

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.
InParanoidiA1A5Q5.
KOiK06709.
OMAiKNTKRMR.
OrthoDBiEOG091G01FR.
PhylomeDBiA1A5Q5.
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.

A1A5Q5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTKSTCAQN PNCSIMIFRP TKEEFNDFDK YIAYMESQGA HRAGLAKVIP
60 70 80 90 100
PKEWRARQSY DNISNILIAT PLQQVVSGQA GVFTQYHKKK KAMTVGQYRH
110 120 130 140 150
LANSKKYQTP PHLDFEDLER KYWKNRLYES PIYGADVSGS LFDGKTQQWN
160 170 180 190 200
VGHLGTIQDL LEQECGIVIE GVNTPYLYFG MWKTSFAWHT EDMDLYSINY
210 220 230 240 250
LHFGQPKTWY AVPPEHGRRL ELLAKELFPG SSQGCQAFLR HKVALISPTV
260 270 280 290 300
LKENGIPFGR ITQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
310 320 330 340 350
GKVASQCSCG EARVSFSMDA FVRILQPERY EMWKRGQDQA VVDHTEAMGP
360 370 380 390 400
TSQELTTWRV IQAPRKTWGL KHLRLRQVSR CLLPVATDSN IANNTQMCHT
410 420 430 440 450
SRQAADSKGD EVQESDPAIA PPYPLGLSSP GHMSTGKRGL GRRPCELGVQ
460 470 480 490 500
ESTNGAPVKR RLPEGRDDRS PSPELQSQSV TGDLIVNSDL VNPGPQHPVT
510
ASEGGLTSDP
Length:510
Mass (Da):57,188
Last modified:January 23, 2007 - v1
Checksum:i3F312BF389E05560
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC128760 mRNA. Translation: AAI28761.1.
RefSeqiNP_001073180.1. NM_001079712.1.
XP_003750480.1. XM_003750432.1.
UniGeneiRn.202733.

Genome annotation databases

EnsembliENSRNOT00000033932; ENSRNOP00000059913; ENSRNOG00000024726.
ENSRNOT00000071532; ENSRNOP00000067344; ENSRNOG00000045905.
GeneIDi100909834.
689582.
KEGGirno:100909834.
rno:689582.
UCSCiRGD:1591045. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC128760 mRNA. Translation: AAI28761.1.
RefSeqiNP_001073180.1. NM_001079712.1.
XP_003750480.1. XM_003750432.1.
UniGeneiRn.202733.

3D structure databases

ProteinModelPortaliA1A5Q5.
SMRiA1A5Q5. Positions 10-345.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000067344.

Proteomic databases

PaxDbiA1A5Q5.
PRIDEiA1A5Q5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000033932; ENSRNOP00000059913; ENSRNOG00000024726.
ENSRNOT00000071532; ENSRNOP00000067344; ENSRNOG00000045905.
GeneIDi100909834.
689582.
KEGGirno:100909834.
rno:689582.
UCSCiRGD:1591045. rat.

Organism-specific databases

CTDi100909834.
55693.
RGDi1591045. Kdm4d.

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiA1A5Q5.
KOiK06709.
OMAiKNTKRMR.
OrthoDBiEOG091G01FR.
PhylomeDBiA1A5Q5.
TreeFamiTF106449.

Miscellaneous databases

PROiA1A5Q5.

Gene expression databases

BgeeiENSRNOG00000024726.
GenevisibleiA1A5Q5. RN.

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_RAT
AccessioniPrimary (citable) accession number: A1A5Q5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2009
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.