Contents 1. Introduction 4304 2. The Active Site 4305 2.1. Ni−Fe Hydrogenases 4306 2.2. Fe−Fe Hydrogenases 4307 2.3. Fe−S Cluster-free Hydrogenases 4307 3. The Redox States of the Active Sites 4307 3.1. Ni−Fe Hydrogenases 4308 3.2. Fe−Fe Hydrogenases 4311 3.3. Fe−S-Cluster-free Hydrogenase (Hmd) 4312 4. Activation Processes 4313 4.1. Ni−Fe Hydrogenases 4313 4.2. Fe−Fe Hydrogenases 4315 5. Inactivation Processes 4316 5.1. Ni−Fe Hydrogenases 4316 5.1.1. Inactivation by O 2 4316 5.1.

In hydrogenases and many other redox enzymes, the buried active site is connected to the solvent by a molecular channel whose structure may determine the enzyme's selectivity with respect to substrate and inhibitors. The role of these channels has been addressed using crystallography and molecular dynamics, but kinetic data are scarce. Using protein film voltammetry, we determined and then compared the rates of inhibition by CO and O2 in ten NiFe hydrogenase mutants and two FeFe hydrogenases. We found that the rate of inhibition by CO is a good proxy of the rate of diffusion of O2 toward the active site. Modifying amino acids whose side chains point inside the tunnel can slow this rate by orders of magnitude. We quantitatively define the relations between diffusion, the Michaelis constant for H2 and rates of inhibition, and we demonstrate that certain enzymes are slowly inactivated by O2 because access to the active site is slow.

[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.