Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector

Many microbes rely on enzymes known as hydrogenases to catalyse the metabolic reactions that generate energy. These enzymes cleave hydrogen molecules to release electrons that go on to participate in further reactions. In order to fully understand how hydrogenases and other enzymes work it is necessary to work out their structure at the atomic level. Last year a technique known as electron cryo-microscopy (cryo-EM) was used to show that Frh—a hydrogenase that is crucial for many different steps in the metabolic process of microbes that produce methane—had a tetrahedral structure. Cryo-EM involves freezing the molecule of interest in a layer of ice to preserve its structure as it is imaged with an electron beam. Unfortunately, the signal-to-noise ratio in each image is low, so researchers must combine many separate images in order to determine the structure of the molecule. The use of a new type of electron detector can improve the performance of an electron cryo-microscope in several ways. Higher frame rates can be used, which makes it possible to correct for movement of the molecule caused by the electron beam. The new electron detectors are also more efficient, so samples can be exposed to lower doses of electrons, reducing damage to the sample. Using the new direct electron detectors, Allegretti et al. were able to work out the structure of Frh in greater detail than before. The results confirm that the previously reported structure is correct. Furthermore, several new structural features were seen for the first time, including a previously unseen ion located between two protein subunits. Allegretti et al. also revealed that the structure of Frh is highly rigid, and so the process by which it catalyses reactions involving its substrate, the coenzyme F420, does not involve changes in its shape. Instead, the reaction rate depends on the rate at which F420 diffuses to the correct position in the enzyme, where the reaction occurs very rapidly.