Reviewed,
UniProtKB/Swiss-Prot Q6B0I6 (KDM4D_HUMAN)
Last modified
November 3, 2009.
Version 46.
History...
Clusters with 100%,
90%,
50% identity |
Documents (6) |
Third-party data |
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Names and origin
| Protein names | 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 names |
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| Organism | Homo sapiens (Human) [Complete proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 523 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence at protein level. |
General annotation (Comments)
| Function | 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. Ref.7 |
| Cofactor | Binds 1 Fe2+ ion per subunit By similarity. |
| Subcellular location | Nucleus By similarity. |
| Sequence similarities | Belongs to the JHDM3 histone demethylase family. Contains 1 JmjC domain. Contains 1 JmjN domain. |
| Caution | It is uncertain whether Met-1 or Met-4 is the initiator. |
Ontologies
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 523 | 523 | Lysine-specific demethylase 4D | PRO_0000234376 | |||||
Regions | |||||||||
| Domain | 18 – 60 | 43 | JmjN | ||||||
| Domain | 146 – 312 | 167 | JmjC | ||||||
| Compositional bias | 91 – 94 | 4 | Poly-Lys | ||||||
Sites | |||||||||
| Metal binding | 192 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 194 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 238 | 1 | Zinc By similarity | ||||||
| Metal binding | 244 | 1 | Zinc By similarity | ||||||
| Metal binding | 280 | 1 | Iron; catalytic By similarity | ||||||
| Metal binding | 310 | 1 | Zinc By similarity | ||||||
| Metal binding | 312 | 1 | Zinc By similarity | ||||||
| Binding site | 136 | 1 | Alpha-ketoglutarate By similarity | ||||||
| Binding site | 202 | 1 | Alpha-ketoglutarate By similarity | ||||||
| Binding site | 210 | 1 | Alpha-ketoglutarate By similarity | ||||||
Amino acid modifications | |||||||||
| Modified residue | 409 | 1 | Phosphoserine Ref.8 | ||||||
Natural variations | |||||||||
| Natural variant | 355 | 1 | S → R: dbSNP rs35631512. | VAR_057882 | |||||
| Natural variant | 408 | 1 | R → Q: dbSNP rs3740853. Ref.1 Ref.4 | VAR_026225 | |||||
| Natural variant | 471 | 1 | A → S: dbSNP rs34366036. | VAR_057883 | |||||
Experimental info | |||||||||
| Sequence conflict | 510 | 1 | H → R in AAH74739. Ref.4 | ||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." 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. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-408. Tissue: Embryo and Teratocarcinoma. |
| [2] | "Human chromosome 11 DNA sequence and analysis including novel gene identification." 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. Sakaki Y.Nature 440:497-500(2006) [PubMed: 16554811] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [3] | 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. Venter J.C.Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [4] | "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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-408. Tissue: Brain. |
| [5] | "The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 395-523. Tissue: Testis. |
| [6] | "Identification and characterization of JMJD2 family genes in silico." Katoh M., Katoh M. Int. J. Oncol. 24:1623-1628(2004) [PubMed: 15138608] [Abstract] Cited for: IDENTIFICATION. |
| [7] | "Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases." Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y. Cell 125:467-481(2006) [PubMed: 16603238] [Abstract] Cited for: FUNCTION, ENZYME ACTIVITY. |
| [8] | "Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis." Wang B., Malik R., Nigg E.A., Korner R. Anal. Chem. 80:9526-9533(2008) [PubMed: 19007248] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-409, MASS SPECTROMETRY. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AK001113 mRNA. Translation: BAA91508.1. Different initiation. AK056162 mRNA. Translation: BAG51636.1. AP002383 Genomic DNA. No translation available. CH471065 Genomic DNA. Translation: EAW66952.1. BC074739 mRNA. Translation: AAH74739.1. BC119010 mRNA. Translation: AAI19011.1. BC122858 mRNA. Translation: AAI22859.1. AL137545 mRNA. Translation: CAB70803.1. | |||||||||||||
| IPI | IPI00017991. | ||||||||||||
| PIR | T46388. | ||||||||||||
| RefSeq | NP_060509.2. | ||||||||||||
| UniGene | Hs.503598 | ||||||||||||
3D structure databases | |||||||||||||
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| ModBase | Search... | ||||||||||||
Protein-protein interaction databases | |||||||||||||
| STRING | Q6B0I6. | ||||||||||||
Proteomic databases | |||||||||||||
| PRIDE | Q6B0I6. | ||||||||||||
Genome annotation databases | |||||||||||||
| Ensembl | ENST00000335080; ENSP00000334181; ENSG00000186280; Homo sapiens. [Genome view] | ||||||||||||
| GeneID | 55693. | ||||||||||||
| KEGG | hsa:55693. | ||||||||||||
| UCSC | uc001pfe.1. human. | ||||||||||||
Organism-specific databases | |||||||||||||
| GeneCards | GC11P094346. | ||||||||||||
| H-InvDB | HIX0010037. | ||||||||||||
| HGNC | HGNC:25498. KDM4D. | ||||||||||||
| MIM | 609766. gene. | ||||||||||||
| PharmGKB | PA134895886. | ||||||||||||
| GenAtlas | Search... | ||||||||||||
Phylogenomic databases | |||||||||||||
| HOVERGEN | Q6B0I6. | ||||||||||||
Gene expression databases | |||||||||||||
| ArrayExpress | Q6B0I6. | ||||||||||||
| Bgee | Q6B0I6. | ||||||||||||
| CleanEx | HS_JMJD2D. | ||||||||||||
| Genevestigator | Q6B0I6. | ||||||||||||
| GermOnline | ENSG00000186280. Homo sapiens. | ||||||||||||
Family and domain databases | |||||||||||||
| InterPro | IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR003349. TF_JmjN. [Graphical view] | ||||||||||||
| Pfam | PF02373. JmjC. 1 hit. PF02375. JmjN. 1 hit. [Graphical view] | ||||||||||||
| SMART | SM00558. JmjC. 1 hit. [Graphical view] | ||||||||||||
| PROSITE | PS51184. JMJC. 1 hit. PS51183. JMJN. 1 hit. [Graphical view] | ||||||||||||
| ProtoNet | Search... | ||||||||||||
Other Resources | |||||||||||||
| SOURCE | Search... | ||||||||||||
Entry information
| Entry name | KDM4D_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q6B0I6 Secondary accession number(s): B3KPC4 Q9NW76 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
| Disclaimer | Any 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. | ||||||||
Relevant documents
| Human chromosome 11 Human chromosome 11: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with


