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Protein

Lysine-specific demethylase 4D

Gene

Kdm4d

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 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

  • chromatin DNA binding Source: MGI
  • damaged DNA binding Source: MGI
  • dioxygenase activity Source: UniProtKB-KW
  • histone demethylase activity Source: MGI
  • histone demethylase activity (H3-K9 specific) Source: MGI
  • metal ion binding Source: UniProtKB-KW

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

ReactomeiR-MMU-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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:3606484. Kdm4d.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • blood microparticle Source: MGI
  • nucleus Source: MGI
  • pericentric heterochromatin Source: MGI
  • site of double-strand break Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 510510Lysine-specific demethylase 4DPRO_0000234377Add
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

PaxDbiQ3U2K5.
PRIDEiQ3U2K5.

PTM databases

PhosphoSiteiQ3U2K5.

Expressioni

Gene expression databases

BgeeiQ3U2K5.
CleanExiMM_JMJD2D.
ExpressionAtlasiQ3U2K5. baseline and differential.
GenevisibleiQ3U2K5. MM.

Interactioni

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000061632.

Structurei

3D structure databases

ProteinModelPortaliQ3U2K5.
SMRiQ3U2K5. Positions 8-338.
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.
InParanoidiQ3U2K5.
KOiK06709.
OMAiPHWARHS.
OrthoDBiEOG7TQV03.
PhylomeDBiQ3U2K5.
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.

Q3U2K5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTKSTCAQN PNCSIMIFRP TKEEFNDFDK YIAYMESQGA HRAGLAKVIP
60 70 80 90 100
PKEWRARQSY DNISNILIAT PLQQVVSGQA GVFTQYHKKK KGMTVGEYRE
110 120 130 140 150
LANSKKYQTP PHLDFEDLER KYWKNRLYES PIYGADVSGS LFDGKTQQWN
160 170 180 190 200
VGHLGTIQDL LEQECGIVIE GVNTPYLYFG MWKTTFAWHT EDMDLYSINY
210 220 230 240 250
LHFGQPKTWY AVPPEHGRRL ERLARELFPG SSQGCQAFLR HKVALISPTV
260 270 280 290 300
LKENGIPFGR ITQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
310 320 330 340 350
GKVASQCSCG EARVSFSMDA FVRILQPERY ELWKRGQDQA VVDHTETMVS
360 370 380 390 400
TSQELTTRRV TKAPRKTWGL KRLRLRQVSR SLLPIATVSN VPCNMQVCHT
410 420 430 440 450
SRQPSDVKGD DVQKSDSARA SPHPLSLPSS GHMSTRRCSL GRRPCELGAQ
460 470 480 490 500
ESSNGAPVKR QLPAGRDDTS PSPELQPQAV SGDLIVDSGL VNPGPQHLMT
510
ASEGGLTSDP
Length:510
Mass (Da):57,212
Last modified:May 16, 2006 - v2
Checksum:i6B57A0300BAD94C9
GO

Sequence cautioni

The sequence BAC26740.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAC26740.1 differs from that shown. Reason: Erroneous termination at position 209. Translated as Trp.Curated
The sequence BAE33135.1 differs from that shown. Reason: Frameshift at position 419. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti374 – 3741R → L in BAC26740 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK030020 mRNA. Translation: BAC26740.1. Sequence problems.
AK155227 mRNA. Translation: BAE33135.1. Frameshift.
CT485607 Genomic DNA. Translation: CAM15687.1.
CT485607 Genomic DNA. Translation: CAX15698.1.
BC112372 mRNA. Translation: AAI12373.1.
CCDSiCCDS22822.2.
RefSeqiNP_775609.2. NM_173433.2.
XP_006510333.1. XM_006510270.2.
XP_006510334.1. XM_006510271.2.
UniGeneiMm.240457.

Genome annotation databases

EnsembliENSMUST00000058796; ENSMUSP00000061632; ENSMUSG00000053914.
GeneIDi244694.
KEGGimmu:244694.
UCSCiuc009oen.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK030020 mRNA. Translation: BAC26740.1. Sequence problems.
AK155227 mRNA. Translation: BAE33135.1. Frameshift.
CT485607 Genomic DNA. Translation: CAM15687.1.
CT485607 Genomic DNA. Translation: CAX15698.1.
BC112372 mRNA. Translation: AAI12373.1.
CCDSiCCDS22822.2.
RefSeqiNP_775609.2. NM_173433.2.
XP_006510333.1. XM_006510270.2.
XP_006510334.1. XM_006510271.2.
UniGeneiMm.240457.

3D structure databases

ProteinModelPortaliQ3U2K5.
SMRiQ3U2K5. Positions 8-338.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000061632.

PTM databases

PhosphoSiteiQ3U2K5.

Proteomic databases

PaxDbiQ3U2K5.
PRIDEiQ3U2K5.

Protocols and materials databases

DNASUi244694.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058796; ENSMUSP00000061632; ENSMUSG00000053914.
GeneIDi244694.
KEGGimmu:244694.
UCSCiuc009oen.1. mouse.

Organism-specific databases

CTDi55693.
MGIiMGI:3606484. Kdm4d.

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ3U2K5.
KOiK06709.
OMAiPHWARHS.
OrthoDBiEOG7TQV03.
PhylomeDBiQ3U2K5.
TreeFamiTF106449.

Enzyme and pathway databases

ReactomeiR-MMU-3214842. HDMs demethylate histones.

Miscellaneous databases

NextBioi386391.
PROiQ3U2K5.
SOURCEiSearch...

Gene expression databases

BgeeiQ3U2K5.
CleanExiMM_JMJD2D.
ExpressionAtlasiQ3U2K5. baseline and differential.
GenevisibleiQ3U2K5. MM.

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

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and NOD.
    Tissue: Testis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "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] OF 106-510.

Entry informationi

Entry nameiKDM4D_MOUSE
AccessioniPrimary (citable) accession number: Q3U2K5
Secondary accession number(s): A2CGB5
, B8JK34, Q2M1G7, Q8BI19
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 16, 2006
Last modified: May 11, 2016
This is version 79 of the entry and version 2 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.