Deserts, Rivers, Pools, and Billabongs: Water Features of the Nitrogenase Proteins, and their Functions

This review examines the occurrence and function of water inside the protein that contains the catalytic site of the enzyme nitrogenase. The requirement of 8 protons and 8 electrons to convert N₂ to NH₃ and the opposing acid-base character of reactant and product are unique in enzymology. The active site is an unprecedented iron sulfide cluster containing one heterometal, in Mo, V, and Fe isozymes. A key component supporting the complex chemical mechanism is water, which transports multiple exogenous protons, sequentially, and assists the egress of hydrophilic ammonia. Using high-resolution crystal structures of the nitrogenase isozymes and cryoEM data, I describe and classify all intraprotein water components. A singular property is the occurrence of extensive anhydrous domains that surround the reaction zone of the cofactor. This focuses attention on the proton supply chain, a river, along which protons are transferred by a Grotthuss mechanism from protein surface to cofactor. Another river, in an opposite direction, runs along the pathway for departing NH₃. I describe mechanisms for translocation of protons and of NH₃ and their use of water and homocitrate. Other water features buried in the proteins include a mechanistically significant single water molecule and featureless water pools.