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UniProtKB/Swiss-Prot entry Q6B0I6


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name KDM4D_HUMAN
Primary accession number Q6B0I6
Secondary accession numbers B3KPC4 Q0VF39 Q9NT41 Q9NW76
Integrated into Swiss-Prot on May 16, 2006
Sequence was last modified on June 16, 2009 (Sequence version 3)
Annotations were last modified on    June 16, 2009 (Entry version 40)
Name and origin of the protein
Protein name Lysine-specific demethylase 4D
Synonyms EC 1.14.11.-
JmjC domain-containing histone demethylation protein 3D
Jumonji domain-containing protein 2D
Gene name
Name: KDM4D
Synonyms: JHDM3D, JMJD2D
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 2: Evidence at transcript level;
References
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT GLN-408.
TISSUE=Embryo, and Teratocarcinoma;
DOI=10.1038/ng1285; PubMed=14702039 [NCBI, ExPASy, EBI, Israel, Japan]
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.;
"Complete sequencing and characterization of 21,243 full-length human cDNAs.";
Nat. Genet. 36:40-45(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
DOI=10.1038/nature04632; PubMed=16554811 [NCBI, ExPASy, EBI, Israel, Japan]
Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T., Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G., Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C., Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A., Hattori M., Rogers J., Lander E.S., Sakaki Y.;
"Human chromosome 11 DNA sequence and analysis including novel gene identification.";
Nature 440:497-500(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.;
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT GLN-408.
TISSUE=Brain;
DOI=10.1101/gr.2596504; PubMed=15489334 [NCBI, ExPASy, EBI, Israel, Japan]
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 395-523.
TISSUE=Testis;
DOI=10.1186/1471-2164-8-399; PubMed=17974005 [NCBI, ExPASy, EBI, Israel, Japan]
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Blocker H., Heubner D., Hoerlein A., Michel G., Wedler H., Kohrer K., Ottenwalder B., Poustka A., Wiemann S., Schupp I.;
"The full-ORF clone resource of the German cDNA consortium.";
BMC Genomics 8:399-399(2007).
[6]
IDENTIFICATION.
PubMed=15138608 [NCBI, ExPASy, EBI, Israel, Japan]
Katoh M., Katoh M.;
"Identification and characterization of JMJD2 family genes in silico.";
Int. J. Oncol. 24:1623-1628(2004).
[7]
FUNCTION, AND ENZYME ACTIVITY.
DOI=10.1016/j.cell.2006.03.028; PubMed=16603238 [NCBI, ExPASy, EBI, Israel, Japan]
Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y.;
"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases.";
Cell 125:467-481(2006).
Comments
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AK001113; BAA91508.1; ALT_INIT; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AK056162; BAG51636.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AP002383; -; NOT_ANNOTATED_CDS; Genomic_DNA.[EMBL / GenBank / DDBJ]
CH471065; EAW66952.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC074739; AAH74739.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC119010; AAI19011.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
BC122858; AAI22859.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AL137545; CAB70803.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
IPI IPI00017991; -.
PIR T46388; T46388.
UniGene Hs.503598
3D structure databases
ModBase Q6B0I6.
Organism-specific databases
GeneCards GC11P094346; -.
H-InvDB HIX0010037; -.
HGNC HGNC:25498; KDM4D.
GenAtlas KDM4D.
MIM 609766; gene. [NCBI / EBI]
PharmGKB PA134895886; -.
Gene expression databases
ArrayExpress Q6B0I6; -.
Bgee Q6B0I6; -.
CleanEx HS_JMJD2D; -.
GermOnline ENSG00000186280; Homo sapiens.
Ontologies
GO
GO:0005634; Cellular component: nucleus (inferred from electronic annotation from UniProtKB-SubCell).
GO:0005506; Molecular function: iron ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0016702; Molecular function: oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (inferred from electronic annotation from UniProtKB-KW).
GO:0008270; Molecular function: zinc ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0016568; Biological process: chromatin modification (inferred from electronic annotation from UniProtKB-KW).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
GO:0006355; Biological process: regulation of transcription, DNA-dependent (inferred from electronic annotation from UniProtKB-KW).
GO:0006350; Biological process: transcription (inferred from electronic annotation from UniProtKB-KW).
QuickGo view.
Family and domain databases
InterPro IPR013129; TF_JmjC.
IPR003347; TF_JmjC_AAH.
IPR003349; TF_JmjN.
Graphical view of domain structure.
Pfam PF02373; JmjC; 1.
PF02375; JmjN; 1.
Pfam graphical view of domain structure.
SMART SM00558; JmjC; 1.
SMART graphical view of domain structure.
PROSITE PS51184; JMJC; 1.
PS51183; JMJN; 1.
PROSITE graphical view of domain structure (profiles).
Proteomic databases
PRIDE Q6B0I6; -.
Genome annotation databases
Ensembl ENSG00000186280; Homo sapiens. [Contig view]
Phylogenomic databases
HOVERGEN Q6B0I6; -.
Other
SOURCE KDM4D; Homo sapiens.
ProtoNet Q6B0I6.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase; Polymorphism; Transcription; Transcription regulation; Zinc.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   523  523     Lysine-specific demethylase 4D. PRO_0000234376
DOMAIN   18    60  43     JmjN. 
DOMAIN   146   312  167     JmjC. 
COMPBIAS   91    94  4     Poly-Lys. 
METAL   192   192        Iron; catalytic (By similarity). 
METAL   194   194        Iron; catalytic (By similarity). 
METAL   238   238        Zinc (By similarity). 
METAL   244   244        Zinc (By similarity). 
METAL   280   280        Iron; catalytic (By similarity). 
METAL   310   310        Zinc (By similarity). 
METAL   312   312        Zinc (By similarity). 
BINDING   136   136        Alpha-ketoglutarate (By similarity). 
BINDING   202   202        Alpha-ketoglutarate (By similarity). 
BINDING   210   210        Alpha-ketoglutarate (By similarity). 
VARIANT   355   355  1     S -> R (in dbSNP:rs35631512 [NCBI]). VAR_057882 
VARIANT   408   408  1     R -> Q (in dbSNP:rs3740853 [NCBI]). VAR_026225 
VARIANT   471   471  1     A -> S (in dbSNP:rs34366036 [NCBI]). VAR_057883 
CONFLICT   510   510        H -> R (in Ref. 4; AAH74739). 
Sequence information
Length: 523 AA [This is the length of the unprocessed precursor] Molecular weight: 58603 Da [This is the MW of the unprocessed precursor] CRC64: 5303A0846ECEBA58 [This is a checksum on the sequence]
        10         20         30         40         50         60 
METMKSKANC AQNPNCNIMI FHPTKEEFND FDKYIAYMES QGAHRAGLAK IIPPKEWKAR 

        70         80         90        100        110        120 
ETYDNISEIL IATPLQQVAS GRAGVFTQYH KKKKAMTVGE YRHLANSKKY QTPPHQNFED 

       130        140        150        160        170        180 
LERKYWKNRI YNSPIYGADI SGSLFDENTK QWNLGHLGTI QDLLEKECGV VIEGVNTPYL 

       190        200        210        220        230        240 
YFGMWKTTFA WHTEDMDLYS INYLHLGEPK TWYVVPPEHG QRLERLAREL FPGSSRGCGA 

       250        260        270        280        290        300 
FLRHKVALIS PTVLKENGIP FNRITQEAGE FMVTFPYGYH AGFNHGFNCA EAINFATPRW 

       310        320        330        340        350        360 
IDYGKMASQC SCGEARVTFS MDAFVRILQP ERYDLWKRGQ DRAVVDHMEP RVPASQELST 

       370        380        390        400        410        420 
QKEVQLPRRA ALGLRQLPSH WARHSPWPMA ARSGTRCHTL VCSSLPRRSA VSGTATQPRA 

       430        440        450        460        470        480 
AAVHSSKKPS STPSSTPGPS AQIIHPSNGR RGRGRPPQKL RAQELTLQTP AKRPLLAGTT 

       490        500        510        520 
CTASGPEPEP LPEDGALMDK PVPLSPGLQH PVKASGCSWA PVP 

Q6B0I6 in FASTA format

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