Xenon and halogenated alkanes track putative substrate binding cavities inthe soluble methane monooxygenase hydroxylase

To investigate the role of protein cavities in facilitating movement of the substrates, methane and dioxygen, in the soluble methane monooxygenase hyd roxylase (MMOH), we determined the X-ray structures of MMOH from Methylococ cus capsulatus (Bath) cocrystallized with dibromomethane or iodoethane, or by using crystals pressurized with xenon gas. The halogenated alkanes bind in two cavities within the alpha -subunit that extend from one surface of t he protein to the buried dinuclear iron active site. Two additional binding sites were located in the beta -subunit. Pressurization of two crystal for ms of MMOH with xenon resulted in the identification of six binding sites l ocated exclusively in the alpha -subunit. These results indicate that hydro phobic species bind preferentially in preexisting cavities in MMOH and supp ort the hypothesis that such cavities may play a functional role in sequest ering and enhancing the availability of the physiological substrates for re action at the active site.