English: Mechanisms of lysinedemethylation by Lysine specific demethylase 1 (LSD1, also known as Lysine demethylase 1A, KDM1A) and by JmjC-domain-containing histone demethylases (JHDMs).
LSD1 first desaturates (oxidizes) the methylated lysine to an imine which is subsequently hydrolyzed to an amine and formaldehyde. LSD1 can only demethylate mono- and dimethylated lysines because trimethylated lysines miss a nitrogen-bound hydrogen (highlighted in green) that could be abstracted to form the imine. The mechanism of imine hydrolysis corresponds to an Alkylimino-de-oxo-bisubstitution in reverse.
LSD1 demethylates H3K4 and H3K9.
JHDMs —- the largest class of demethylase enzymes —- form a highly reactive oxoferryl species in presence of α-ketoglutarate (αKG) and oxygen that hydroxylates the methyl group. The resulting hydroxymethylamine spontaneously decomposes to an amine and formaldehyde. Demethylases of the JHDM class demethylate H3K9 and H3K36.
References:
Klose RJ, Kallin EM, Zhang Y (2006). "JmjC-domain-containing proteins and histone demethylation". Nature Reviews Genetics7 (9): 715–727. DOI:10.1038/nrg1945. PMID16983801.
Markolovic S, Leissing TM, Chowdhury R, Wilkins SE, Lu X, Schofield CJ (2016). "Structure–function relationships of human JmjC oxygenases—demethylases versus hydroxylases". Current Opinion in Structural Biology41: 62–72. DOI:10.1016/j.sbi.2016.05.013. PMID27309310.
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