gocentral
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18 years ago Logged In: YES user_id=775618
Talked briefly with Karen this morning about this NTR and H2-K4 related term and just wanted to suggest that these could be modeled similar to the function terms for histone lysine N-methyltransferases (see for example GO function terms 42800, 46975, 46976, 42799 and 31151 and upper level terms 18024 and 42054.
Cheers, Rob
Original comment by: rnash
Hi,
I need a new term for a specific histone demethylase in the function ontology. We don't seem to have any histone demethylase terms, or even much in the way of protein demethylase terms. The EC classification doesn't seem to have them either, so I've already submitted a report suggesting the addition of the one that the paper I read characterized. I'm asking for 1 specific term with this request, but the paper I read discussed a previously characterized activity that is different, so I also put some info about that here since it seems that we should at least have a term for the activity.
As I said, for the one I need, I have already submitted a report to the Enzyme Commission, copied here. I think you can get the term name and a definition out of that. Right now, it might just have to go under 'catalytic activity' because I have no idea where it belongs, but once the EC has added it, we could just move it appropriately.
thanks,
-Karen
REPORT FORM FOR AN ENZYME NOT CURRENTLY INCLUDED IN "ENZYME NOMENCLATURE"
Proposed name(s): Primary name: histone-lysine(H3-K36) demethylase
Reaction catalysed: methyl-lysine + alpha-ketoglutarate + O2 --> succinate + CO2 + HCHO + lysine
can also demethylate dimethyl-lysine to monomethyl-lysine
Subclass in Enzyme Nomenclature proposed: no idea
Source of enzyme: Organism: human, S. cerevisiae
Cofactor requirement(s): Fe(II)
Brief comment on specificity: "We analysed its site specificity using histone substrates radiolabelled at all known methylated sites in histones H3 (K4, K9, K27, K36, K79) and H4 (K20, R3). Of the seven substrates, only H3-K36 methylated by Set2 was a substrate for JHDM1A."
Other comments:
They refer to the human protein as FBXL11, but when I search Entrez for that name, I get two entries. Because I am not sure which they used, I have put a quote from the paper here, rather than guessing which accession number is correct.
"Because histone demethylase activity is the first function attributed to FBXL11 and because FBXL11 is the first JmjC domain-containing protein shown to possess histone demethylase activity, we have named the protein JHDM1A (JmjC domain-containing histone demethylase 1A.). The highly related protein FBXL10, which we have named JHDM1B (Supplementary Fig. S3a), is also an active H3-K36 demethylase (data not shown)."
References: Tsukada YI, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, Zhang Y (2005) Histone demethylation by a family of JmjC domain-containing proteins. Nature (epub ahead of print) PubMed ID:16362057
quote from paper about other histone demethylase activity:
Using a candidate approach, it has been demonstrated that LSD1/ BHC110, a nuclear amine oxidase homologue previously found in several histone deacetylase complexes8, 9, 10, can specifically demethylate monomethyl-H3-K4 (H3K4me1) and H3K4me2 in a FAD (flavin adenine dinucleotide)-dependent oxidative reaction.
Hakimi, M. A. et al. A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. Proc. Natl Acad. Sci. USA 99, 7420–7425 (2002)
Shi, Y. et al. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature 422, 735–738 (2003)
You, A. , Tong, J. K. , Grozinger, C. M. & Schreiber, S. L. CoREST is an integral component of the CoREST-human histone deacetylase complex. Proc. Natl Acad. Sci. USA 98, 1454–1458 (2001)
Reported by: krchristie
Original Ticket: "geneontology/ontology-requests/3122":https://sourceforge.net/p/geneontology/ontology-requests/3122