Hydrogenase enzymes cycle

Figure 3 Speculative model for the hydrogenase enzyme cycle such as that from D. gigas. The highest oxidation states of the enzyme are at the top, and each step down corresponds to a one-electron reduction. Some hydrons that are transferred to sites in the protein are not shown. Redox states of the iron-sulfur clusters are omitted.

The above electron and proton transfers complete one cycle of the hydrogenase enzyme. The entire mechanism as suggested above is... 

The electrons then are used by a hydrogenase enzyme to produce Ha gas. Desuljovibrio can also convert succinate, fumarate, malate, oxaloacetate, or lactate into pyruvate by reactions which resemble fragments of the Krebs cycle (360). 

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedraHy coordinated by a combination of thiolate and sulfide donors. Of the 10 or more stmcturaHy characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein mbredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane stmctures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane stmcture (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH at a MoFe Sg homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

Moreover, an electron transfer chain could be reconstituted in vitro that is able to oxidize aldehydes to carboxylic acids with concomitant reduction of protons and net production of dihydrogen (213, 243). The first enzyme in this chain is an aldehyde oxidoreductase (AOR), a homodimer (100 kDa) containing one Mo cofactor (MOD) and two [2Fe—2S] centers per subunit (199). The enzyme catalytic cycle can be regenerated by transferring electrons to flavodoxin, an FMN-con-taining protein of 16 kDa (and afterwards to a multiheme cytochrome and then to hydrogenase) ... 

Fig. 5.7. In green sulfur bacteria and in some archaebacteria, a reverse citric acid cycle is used for the assimilation of C02. It must be assumed that this was the original function of the citric acid cycle that only secondarily took over the role as a dissimulatory and oxidative process for the degradation of organic matter. A major enzyme here is 2-oxoglutarate ferredoxin for C02 fixation. Note that it, like several other enzymes in the cycle, uses Fe/S proteins. One is the initial so-called complex I which has eight different Fe/S centres of different kinds but no haem (see also other early electron-transfer chains, e.g. in hydrogenases).

We should also remember that not all of the states that we see when freezing the enzyme (Section 7.4) are necessarily part of the mechanism. The most stable enzyme molecule is a dead one, so we must be aware that some of the spectroscopic signals represent damaged molecules. In the [NiFe] hydrogenases, the NiA and NiB states probably are not involved in the catalytic cycle, because they react slowly, if at all, with H2. In the mechanism shown in Fig. 8.3, it is assumed that the relevant active states are NiSR, NiA and NiR. 

Fig. 10. Hypothetical reaction cycle for D. gigas hydrogenase, based on the EPR and redox properties of the nickel (Table II). Only the nickel center and one [4Fe-4S] cluster are shown. Step 1 enzyme, in the activated conformation and Ni(II) oxidation state, causes heterolytic cleavage of H2 to produce a Ni(II) hydride and a proton which might be associated with a ligand to the nickel or another base in the vicinity of the metal site. Step 2 intramolecular electron transfer to the iron-sulfur cluster produces a protonated Ni(I) site (giving the Ni-C signal). An alternative formulation of this species would be Ni(III) - H2. Step 3 reoxidation of the iron-sulfur cluster and release of a proton. Step 4 reoxidation of Ni and release of the other proton.

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