News > BIO > Fall 2007

Structural biology

Breaking point

Researchers explore how a key enzyme uses oxygen to get a job done

How does it work? For centuries biologists have been asking that question about everything from meiosis to memory. For more than three decades, John Lipscomb, a professor in the Department of Biochemistry, Molecular Biology and Biophysics, has been asking it about biological molecules that use metal atoms to help them carry out difficult chemical reactions. Some of these so-called “metalloenzymes” use oxygen to crack open small, ring-shaped molecules. This ring-cracking is an integral part of diverse and important processes such as metabolizing food, ripening bananas and breaking down pollutants.

“Oxygen is a very potent chemical, and we live in a sea of it,” he says. “Metalloenzymes allow oxygen to be used safely, and ultimately they are why we can exist on this planet.”

Working with Lipscomb on understanding how metalloenzymes and oxygen interact is postdoctoral student Elena Kovaleva, a second-generation biochemist from Russia who has been fascinated by enzymes since her undergraduate days.

Recently, Lipscomb and Kovaleva made a huge leap forward in understanding the actions of a metalloenzyme called 2,3-HPCD, which helps bacteria break down certain hard-to-degrade organic molecules. Elucidating the mechanism for the enzyme is valuable, Lipscomb says, because it sheds new light on how molecular oxygen is used precisely when and where it is needed. It also provides insights that other researchers can use as they work to understand other reactions that use oxygen.

To learn how the enzyme does its job, Kovaleva applied an innovative technique pioneered by associate professor Carrie Wilmot that involves starting the reaction in a crystal, which causes it to halt in mid-move like a player in a game of molecular freeze-tag. When Kovaleva did this with 2,3-HPCD, she discovered that the reactions at three of the enzyme’s four iron atoms were frozen at different steps of the process.

One of the in-between states held a big surprise: Rather than binding to the iron by just one of its two atoms, as had been thought, the oxygen molecule bound sideways, placing it in perfect position to react with the ring molecule bound next to it. A second in-between state revealed a long-suspected, but never observed, intermediate in which the oxygen is seen actually reacting with the ring molecule while both are still bound to the iron.

“Nobody expected to ever be able to see this intermediate,” Lipscomb says. “It defines the chemistry of the class.”

Lipscomb and Kovaleva are now working to understand how various parts of the enzyme near the iron facilitate the reaction. They’re also exploring the role of molecular-scale motion in the process, and are looking to apply Wilmot’s technique to analyze other metalloenzymes. “I am always surprised by how many new research directions come to light after each new discovery,” Lipscomb says.

—Mary Hoff