The methenyl group originated as CO2 before being incorporated into the substrate, which is catalytically reduced by H2 to methylenetetrahydromethanopterin as shown.
Between species the enzyme is found with differing numbers of sub-units and some minor amino acid sequence variations.
In addition the 542 Da compound can be further degraded by a phosphodiesterase (which specifically cleaves phosphate bonds).
On the basis of spectroscopic characterization, Shima et al. have proposed a structure for this organic cofactor (minus the iron atom and CO molecules) as shown:[4]
Although the mechanism by which Hmd acts is unknown, the iron-containing cofactor is in part responsible for the catalytic activity.
It has been proposed that the iron functions to bind H2 and the substrate methenyltetrahydromethanopterin, organizing these two reactants in close proximity.