Ar. George et al., A COMPUTATIONAL INVESTIGATION OF THE POSSIBLE SUBSTRATE-BINDING SITESIN THE HYDROXYLASE OF SOLUBLE METHANE MONOOXYGENASE, Journal of molecular catalysis. B, Enzymatic, 2(2-3), 1996, pp. 103-113
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.