Methanotrophic bacteria consume 30 million metric tons of methane per year and have captivated researchers for their natural ability to convert the potent greenhouse gas into usable fuel. Yet we know very little about how the complex reaction occurs, and this limits our ability to use the double benefit to our advantage. By studying the enzyme—particulate methane monooxygenase (pMMO)—that the bacteria use to catalyze the reaction, a team at Northwestern University has now discovered key structures that may drive the process, and suggest that their findings could ultimately lead to the development of human-made biological catalysts that convert methane gas into methanol.

“If we don’t understand exactly how the enzyme performs this difficult chemistry, we’re not going to be able to engineer and optimize it for biotechnological applications,” said Northwestern’s Amy Rosenzweig, PhD, senior author of the team’s published paper in Science. “Methane has a very strong bond, so it’s pretty remarkable there’s an enzyme that can do this … If you want to optimize the enzyme to plug it into biomanufacturing pathways or to consume pollutants other than methane, then we need to know what it looks like in its native environment and where the methane binds … You could use bacteria with an engineered enzyme to harvest methane from fracking sites or to clean up oil spills.”

Scientists have engineered methanotrophs to produce a range of products, but low yields and poor conversion efficiencies mean the processes aren’t economically viable, the team explained. “For methane bioconversion to be transformative, the initial step—oxidation of methane to methanol—must be optimized, which requires molecular-level understanding of the main enzyme responsible, particulate methane monooxygenase (pMMO).” “The enzyme comprises PmoA (β), PmoB (α), and PmoC (γ), arranged as a trimer of αβγ protomers,” the investigators further noted. “The crystal structures of detergent-solubilized pMMO from multiple methanotrophic species have revealed the presence of three copper-binding sites.”

However, pMMO, a copper-dependent enzyme, is a particularly difficult protein to study because it’s embedded in the bacterial cell membrane. Typically, when researchers study methanotrophic bacteria they use a harsh process in which the proteins are ripped out of the cell membranes using a detergent solution. While this procedure effectively isolates the enzyme, it also kills all enzyme activity and limits how much information researchers can gather—like monitoring a heart without the heartbeat. “pMMO activity decreases upon solubilization in detergent, and purified samples exhibit zero methane oxidation activity, which means that the structures do not represent the active enzyme,” the scientists commented. “Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site.”