Hydrogenase mechanism

George SJ, Cui Z, Razavet M, Pickett CJ (2002) The di-Iron subsite of all-iron hydrogenase mechanism of cyanation of a synthetic 2Fe3S -carbonyl assembly. Chem. Eur. J. 8 4037 1046... 

Figure 10.1. Structural components in the hydrogenase mechanism, shown for H2 - 2H+ + 2e in NiFe active sites. The reversible electron pathway is facilitated by three Fe-S clusters that act as stepping stones-to the surface of the small subunit, where there is a potential docking site for a c-type cytochrome. The proton channel is proposed to consist of a chain of proton-carrying amino acid residues leading to the surface of the large subunit. Channels for H2 ingress/egress have been identified.

Spectroscopic studies have been instrumental in elucidating the catalytic mechanism of Ni-Fe hydrogenases. A great deal of controversy concerning this mechanism arises from the fact that, as the as the X-ray crystallographic analysis has shown, there are at least three potential redox-active species at the enzyme s active site the thiolate ligands (75) and the Fe (65) and Ni (9) ions. 

The biologically uncommon Ni center associated with FeS clusters is a powerful and unique catalytic unity. In this chapter we have reviewed the structural and mechanistic aspects of three NiFeS centers the active site of hydrogenase and Clusters A and C of CODH/ACS. In the former, the association of a Ni center with the most unusual FeCOCN2 unit is a fascinating one. Model chemists, spectroscopists, and crystallographers have joined efforts to try and elucidate the reaction mechanism. Although a consensus is being slowly reached, the exact roles of the different active site components have not yet been fully established. Ni appears to be the catalytic center proper, whereas the unusual Fe center may be specially suited to bind a by-... 

In the same year, Evans and coworkers reported the electrochemical reduction of protons to H2 catalyzed by the sulfur-bridged dinuclear iron complex 25 as a hydrogenase mimic in which acetic acid was used as a proton source [201]. The proposed mechanism for this reaction is shown in Scheme 60. The reduction of 25 readily affords 25 via a one electron reduction product 25. Protonation... 

The proposed mechanism of H2 evolution by a model of [FeFeJ-hydrogenases based upon DFT calculations [204-206] and a hybrid quanmm mechanical and molecular mechanical (QM/MM) investigation is summarized in Scheme 63 [207]. Complex I is converted into II by both protonation and reduction. Migration of the proton on the N atom to the Fe center in II produces the hydride complex III, and then protonation affords IV. In the next step, two pathways are conceivable. One is that the molecular hydrogen complex VI is synthesized by proton transfer and subsequent reduction (Path a). The other proposed by De Gioia, Ryde, and coworkers [207] is that the reduction of IV affords VI via the terminal hydride complex V (Path b). Dehydrogenation from VI regenerates I. 

Scheme 65 The calculated mechanism of H-H bond cleavage reaction of the model complex for [Fe] -hydrogenases...

A different mechanism for reduction processes by [Fe]-hydrogenase 56 is assumed. The hydride generated by splitting dihydrogen is directly transferred to an electrophilic organic center in methenyltetrahydrocyanopterin. As no electrons need to be transferred this reaction requires only one metal center. Due to its structure the center of [Fe]-hydrogenase 56 does not count to the class of ferrates. 

Scheme 13 Model complexes for [FeFe]-hydrogenase 4 (right) and proposed mechanisms for electrocatalytic hydrogen generation (left) (a) EECC mechanism, (b) ECCE mechanism PTA = phosphatriazaadamantane [33]...

Amara, P., Volbeda, A., Fontecilla-Camps, J. C., Field, M. J., 1999, A Hybrid Density Functional Theory/Mo-lecular Mechanics Study of Nickel-Iron Hydrogenase Investigation of the Active Site Redox States , J. Am. Chem. Soc., 121, 4468. 

Knowledge of the active site allows for speculation on the mechanism of H2-D20 exchange which these Fe4 systems catalyze 473,483). Ruthe-nium(III) systems catalyze such an exchange via a ruthenium(III) hydride intermediate (7, p. 73 Section II,A), as exemplified in reactions (82) and (83), and iron hydrides must be involved in the hydrogenase systems. Ruthenium(III) also catalyzes the H2 reduction of ruthenium(IV) via reaction (82), followed by reaction (84) (3), and using these ruthenium systems as models, a very tentative scheme has been proposed 473) for... 

Proposed mechanism for the reversible reaction of N, N -methenyltetrahydromethanopterin (methenyl-H4MPT ) with H2 to N, N -methylenetetrahydromethanopterin (methylene-H4MPT) and a proton catalysed by the metal-free hydrogenase from methanogenic archaea... 

The simple-looking task is solved by a sophisticated molecular mechanism. Hydrogenase is a metalloenzyme, harbouring Ni and Fe atoms. Like most metalloenzymes, hydrogenases are extremely sensitive to inactivation by oxygen, high temperature and other environmental factors. These properties are not favourable for several potential biotechnological applications. 

The ability to catalyse the evolution or oxidation of H2 may have been exploited by the earliest life forms as H2 would have been present in the early prebiotic environments. The origins of the proton-dependent chemiosmotic mechanism for ATP synthesis may also reflect the formation of proton gradients created by hydrogenases on either side of the cytoplasmic membrane. In addition, it has been speculated that the coupling of H2 and S metabolisms was also of fundamental importance in the origin of life. These two processes seem intimately coupled in the bifunctional sulfhydrogenase found in Pyrococcus furiosus (a combination of subunits for hydrogenase and sulfite reductase) which can dispose of excess reductant either by the reduction of protons to H2 or S° to H2S (Ma et al. 1993 Pedroni et al. 1995). 

Aerobic bacteria which often use H2 as an alternative energy source express hydrogenase genes, with a few exceptions, when the substrate is provided (Table 3.1). How do these organisms recognize the presence of H2, the smallest molecule on Earth The underlying molecular mechanisms are subject of current research and will be discussed in Sections 3.2 and 3.3. 

Isotope-exchange reactions can provide incisive information about the mechanisms by which hydrogenases catalyse their reactions. The ratios of products formed, and in the rates of reaction with different isotopes, can be measured. Different hydrogenases show significantly different proportions of and H HO produced in reactions (3) and (4), and this effect has been used to identify the different types of hydrogenases in whole cells, without the need for purification (Berber et al. 1987). 

The cytoplasmic NAD-reducing hydrogenase (SH) of the bacterium R. eutropha is a heterotetrameric enzyme, which contains several cofactors (Friedrich et al. 1996 Thiemermann et al. 1996). The Ni-containing subunit is called HoxH. This subunit plus the small subunit HoxY form the strictly conserved hydrogenase module with the Ni-Fe centre and a proximal [4Fe-4S] cluster. HoxF and HoxU represents the Fe-S/flavoprotein moiety which is closely related to a similar moiety in NADHrubiquinone oxidoreductase. The SH has been subject to molecular biological techniques in order to study its modular structure, mechanism and biosynthesis. 

---