Human Gene KDM2A (uc001ojw.3) Description and Page Index
Description: Homo sapiens lysine (K)-specific demethylase 2A (KDM2A), transcript variant 1, mRNA. RefSeq Summary (NM_012308): This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]. Transcript (Including UTRs) Position: hg19 chr11:66,886,740-67,025,550 Size: 138,811 Total Exon Count: 21 Strand: + Coding Region Position: hg19 chr11:66,888,788-67,022,526 Size: 133,739 Coding Exon Count: 20
ID:KDM2A_HUMAN DESCRIPTION: RecName: Full=Lysine-specific demethylase 2A; EC=22.214.171.124; AltName: Full=CXXC-type zinc finger protein 8; AltName: Full=F-box and leucine-rich repeat protein 11; AltName: Full=F-box protein FBL7; AltName: Full=F-box protein Lilina; AltName: Full=F-box/LRR-repeat protein 11; AltName: Full=JmjC domain-containing histone demethylation protein 1A; AltName: Full=[Histone-H3]-lysine-36 demethylase 1A; FUNCTION: Histone demethylase that specifically demethylates 'Lys- 36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys- 36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. CATALYTIC ACTIVITY: Protein N(6),N(6)-dimethyl-L-lysine + 2- oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2). CATALYTIC ACTIVITY: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2). COFACTOR: Binds 1 Fe(2+) ion per subunit. SUBUNIT: Part of a SCF (SKP1-cullin-F-box) protein ligase complex (By similarity). Interacts with CBX5/HP1A; the interaction promotes CBX5 localization to chromatin. SUBCELLULAR LOCATION: Nucleus, nucleoplasm. Note=Punctate expression throughout the nucleoplasm and enriched in the perinucleolar region. Specifically nucleates at CpG islands where it's presence results in chromatin depleted in H3K36me2. TISSUE SPECIFICITY: Widely expressed, with highest levels in brain, testis and ovary, followed by lung. DOMAIN: The JmjC domain mediates demethylation activity and is required for satellite silencing. DOMAIN: The CXXC zinc finger preferentially recognizes nonmethylated CpG DNA, and binding is blocked when the CpG DNA is methylated. PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. SIMILARITY: Belongs to the JHDM1 histone demethylase family. SIMILARITY: Contains 1 CXXC-type zinc finger. SIMILARITY: Contains 1 F-box domain. SIMILARITY: Contains 1 JmjC domain. SIMILARITY: Contains 6 LRR (leucine-rich) repeats. SIMILARITY: Contains 1 PHD-type zinc finger. SEQUENCE CAUTION: Sequence=AAD56012.1; Type=Erroneous initiation; Sequence=BAA76848.2; Type=Erroneous initiation; Sequence=BAB15795.1; Type=Frameshift; Positions=410;
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q9Y2K7
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.