A COMPUTATIONAL INVESTIGATION OF THE POSSIBLE SUBSTRATE-BINDING SITESIN THE HYDROXYLASE OF SOLUBLE METHANE MONOOXYGENASE

In this paper we report docked conformations for a diverse range of su bstrates within the hydroxylase component of soluble methane monooxyge nase (sMMO). Based on energy minimisation calculations, three substrat e binding sites have been elucidated. There is a unique site at which the lowest binding energy structures for methane, the in vivo enzyme s ubstrate, acetylene (a potent suicide substrate), propene and pyridine are located, These four are designated group I substrates. The unique site is approximately 3 Angstrom from the diiron site so that substra te oxidation can be easily achieved, The orientation of each of the gr oup I molecules in the unique site reflects precisely the observed pro duct formed in the oxidation reaction, Substrates whose molecular volu mes are greater than approximate to 71 Angstrom(3) are not accommodate d 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 Angstrom from each of the iron atoms of the active site, The energ y 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 grou p 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-ore speci es. The required conformational change may be initiated by the regulat ory protein B binding to the hydroxylase.