A computational investigation of the possible substrate binding sites in the hydroxylase of soluble methane monooxygenase

Abstract

In this paper we report docked conformations for a diverse range of substrates within the hydroxylase component of soluble methane monooxygenase (sMMO). Based on energy minimisation calculations, three substrate binding sites have been elucidated. There is a unique site at which the lowest binding energy structures for methane, the in vivo enzyme substrate, acetylene (a potent suicide substrate), propene and pyridine are located. These four are designated group I substrates. The unique site is approximately 3 Å from the diiron site so that substrate oxidation can be easily achieved. The orientation of each of the group I molecules in the unique site reflects precisely the observed product formed in the oxidation reaction. Substrates whose molecular volumes are greater than ≈ 71 Å 3 are not accommodated at the unique binding site. Rather, these group II molecules cluster at two further sites, termed A and B, both of which are approximately 14 Å from each of the iron atoms of the active site. The energy differences for binding of group II substrates at either site A or B are not great. Larger molecules bind preferentially at B, but size is not the only discriminatory factor between sites A and B. As the group II molecules are known sMMO substrates, a conformational change must occur which opens paths between sites A and B and the unique site to permit oxidation of these substrates by the high valent iron-oxo species. The required conformational change may be initiated by the regulatory protein B binding to the hydroxylase.