Soluble methane monooxygenase requires complexes between its three component proteins for efficient catalysis. The hydroxylase (MMOH) must bind both to the reductase (MMOR) and to the regulatory protein (MMOB) to facilitate oxidation of methane to methanol. Although structures of MMOH, MMOB, and one domain of MMOR have been determined, less geometric information is available for the complexes. To address this deficiency, MMOH and MMOR were cross-linked by a carbodiimide reagent and analyzed by specific proteolysis, matrix-assisted laser desorption/ionization time-offlight mass spectrometry, and capillary high performance liquid chromatography mass spectrometry. Tandem mass spectra conclusively identified two amine-to-carboxylate cross-linked sites involving the ␣ subunit of MMOH and the [2Fe-2S] domain of MMOR (MMOR-Fd). In particular, the N terminus of the MMOH ␣ subunit forms cross-links to the side chains of MMOR-Fd residues Glu-56 and Glu-91. These Glu residues are close to one another on the surface of MMOR-Fd and >25 Å from the [2Fe-2S] cluster. Because the N terminus of the ␣ subunit of MMOH was not located in the crystal structure of MMOH, a detailed structural model of the complex based on the cross-link was precluded; however, a previously proposed binding site for MMOR on MMOH could be ruled out. Based on the cross-linking results, a MMOR E56Q/E91Q double mutant was generated. The mutant retains >80% of MMOR NADH oxidase activity but reduces sMMO activity to ϳ65% of the level supported by the wild type reductase. Cross-linking to MMOH was diminished but not abolished in the double mutant, indicating that other residues of MMOR also form cross-links to MMOH.Methanotrophic bacteria rely on metalloenzymes to catalyze methane hydroxylation (Equation 1), the first step in the metabolic pathway that supplies all their cellular carbon and energy.Methanotrophs express a membrane-bound enzyme termed particulate methane monooxygenase to convert methane to methanol. When copper is unavailable some methanotrophs, including Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b, employ an iron-containing soluble methane monooxygenase (sMMO) 1 (1). The sMMO system comprises several proteins. The ␣ 2  2 ␥ 2 hydroxylase (MMOH, 251 kDa) contains a glutamate-bridged diiron active site in each ␣ subunit. The crystal structure of MMOH has been determined in several redox states and with various products and substrate analogs bound (2-6). An ironsulfur flavoprotein reductase (MMOR, 38.5 kDa) transfers electrons from NADH to MMOH. The solution structure of the N-terminal [2Fe-2S] domain of MMOR is available (7). A cofactorless regulatory protein (MMOB, 15.9 kDa) alters the properties of the diiron site and is required for activity, and its solution structure has also been determined (8, 9). A fourth protein (MMOD (component D of sMMO), 11.9 kDa) binds to the hydroxylase and inhibits catalysis in vitro, but its function has yet to be determined (1, 10).Complex formation between MMOH, MMOR, and MMOB is required...