Hydrogenase substrate binding

Toxic ligands (CO, NO, CN, F , H2S) can bind to metals in the active site of enzymes, thus inhibiting substrate binding, or coordinate to more readily available metal ions, thereby blocking the proper biological function of the metal. However, recent research suggests that such molecules are essential to several hydrogenases (see Chapters 8 and 9). 

Figure 3.4.11 Synthetic molecular catalysts for hydrogen conversion. (A) [FeFe] hydrogenase model with functionalities for substrate binding (H2) and management of redox and proton equivalents (adapted from [162]). (B) Synthetic mononuclear Ni electrocatalyst with pending amines that function as proton relays proposed transition state for heterolytic H2 splitting and formation (adapted from [165]).

Camara JM, Rauchfuss TB. Combining acid-base, redox and substrate binding functionalities to give a complete model for the [FeFe]-hydrogenase. Nat Chem. 2012 4 (1) 26—30. 

It is now widely appreciated that the old, established view of Fe-S clusters as a class of integral structural units whose activity is limited to electron transfer is in error. We have become aware of other roles. For example, in the Fe-hydrogenases, it is certain that a cluster serves as the catalytic site with which the Hj/H substrates interact [164]. Moreover, following the discovery by Beinert s group that aconitase is an Fe-S protein [175], there are now further examples of clusters occurring in enzymes that do not catalyze, at least obviously, a redox reaction. With aconitase itself, it is established that substrates bind to one Fe subsite of a [4Fe-4S] cluster without major disturbance of the core structure [189]. Such findings demonstrate that real chemistry is available, reactivity that may be exploited once tuned by the protein environment. 

Compared to most enzymes, which often undergo considerable conformational changes on binding of the substrates, hydrogenases are rather rigid proteins. The substrates are small and mobile, and can penetrate to the active site. Probably the only parts of the enzyme that move significantly are amino acid side-chains and bound water molecules involved in transfer of hydrons to the active site (Fig. 8.1). 

Such a metabolism ( fumarate respiration ) is well known from anaerobic mitochondria (Tielens et al. 2002 Tielens and van Hellemond, Chap. 6 in this volume), but is unique in combination with a hydrogenase that might compete with the fumarate reductase for the same substrates. This hydrogenase of N. ovalis represents a novel type of [Fe]-only or [FeFe]-hydrogenase that allows H2 formation to be coupled directly to the reoxidation of NADH. The [Fe]-hydrogenase is linked covalently with a protein, which possesses NAD and FMN binding sites, and a ferredoxin-like FeS module that allows transfer... 

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