Hydrogenases iron-sulfur clusters

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. 

Fig. 8. The structure of D. gigas hydrogenase showing the novel heterodinuclear [NiFe] site, the three iron-sulfur clusters, and the tracing of the polypeptide chain...

Brazzolotto X, JK Rubach, J Gaillard, S Gambrelli, M Atta, M Fontecave (2006) The [Fe-Fe]-hydrogenase maturation protein HydF from Thermotoga maritima is a GTPase with an iron-sulfur cluster. J Biol Chem 279, 281 769-774. 

The third type of hydrogenases from some methanogenic archea, also referred to as iron-sulfur-cluster-free hydrogenase, oxHmd, has attracted interest in bioinorganic... 

Fig. 5.4(a). Structures of iron-sulfur clusters found in proteins, (b) An hydrogenase active site. Note the presence of CO and CN ligands, which could have been present in the primitive anaerobic environment. 

Activities and states of the [NiFe] centre and iron-sulfur clusters in the [NiFe] hydrogenase of D. gigas... 

Two [Fe] hydrogenase structures have so far been determined from C. pasteurianum (Cp) (Peters et al. 1998) and D. desulfuricans (Dd) (Nicolet et al. 1999). They have in common a large domain, which contains the catalytic site and three [4Fe-4S] iron sulfur clusters. The catalytic site and the closest (proximal) cluster are deeply buried inside the protein between two domains (or lobes), with access to a third, ferredoxin-like, domain that contains the two remaining (medial and distal) clusters. By contrast with [NiFe] hydrogenases the proximal [4Fe-4S] cluster is directly bridged to the bin-uclear active site by a cysteic thiolate (Fig. 6.12). 

EPR and Mossbauer spectroscopies have been successfully used to characterize iron-sulfur clusters. Hydrogenases are no exception. Here, we will describe the knowledge gained from applying these spectroscopies to the study of [NiFe] hydrogenase. 

Figure 8.3 Outline reaction cycle of NiFe hydrogenase.The minimal hydrogenase is depicted, consisting of the [NiFe] centre in the large subunit, and the proximal [4Fe-4S] cluster (C) in the small subunit.The reaction is written in the direction of the oxidation of H2. Electrons are transferred out through the other iron-sulfur clusters to an acceptor protein (not shown).The equivalent states of the NiFe centre B, SR, R and C are indicated. Reduced centres are shaded. Electron transfers are accompanied by transfers of hydrons (not shown).

Figure 10.3 Z-scheme of oxygenic photosynthesis in green algae and cyanobacteria, showing links to hydrogenase. Q (plastoquinone) and X (an iron-sulfur cluster) are electron acceptors from photosystems II and I, respectively.The two hydrogenases shown are the NADP-dependent bidirectional hydrogenase and a ferredoxin-dependent enzyme.

Adams, M. W., Eccleston, E. and Howard, J. B. (1989) Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum. Proc. Natl. Acad. Sci. USA, 86, 4932-6. 

Erbes, D. L., Burris, R. H. and Orme-Johnson, W. H. (1975) On the iron-sulfur cluster in hydrogenase from Clostridium pasteurianum W5. Proc. Natl. Acad. Sci. USA, 72, 4795-9. 

Zirngibl, C., van Dongen, W., Schworer, B., von Biinau, R., Richter, M., Klein, A., Thauer, R. K. (1992) H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase with iron-sulfur clusters in methanogenic archaea. Eur. J. Biochem. 208, 511-20. 

Pereira AS, Tavares P, Moura I, et al. 2001. Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio vulgaris hydrogenase. I Am Chem Soc 123 2771-82. 

Korbas M, Vogt S, Meyer-Klaucke W, Bill E, Lyon EJ, Thauer RK, Shima S (2006) The iron-sulfur cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif. J Biol Chem 281 30804-30813... 

Both hydrogenases and carbon monoxide oxidoreductases contain iron-sulfur clusters in addition to nickel. It may be noted that in addition to the Ni hydrogenases, there is another class of Fe hydrogenases, such as those in clostridia, which contain no nickel but have a specialized type of iron-sulfur cluster (28a, 28b). Therefore, it has to be established that the nickel in Ni hydrogenases is the active site as will be seen later, there is a considerable amount of circumstantial evidence for this. 

The EPR-detectable iron-sulfur clusters of N. opaca hydrogenase are associated with the NAD-reducing segment of the enzyme. 

Fig. 7. Optical absorption and magnetic circular dichroism spectra of oxidized hydrogenase from M. thermoautotrophicum (AH strain), nickel concentration 120 pM. (a) Optical absorption spectrum, at room temperature the absorption is predominantly due to iron-sulfur clusters, (b) MCD spectra recorded at 1.53, 4.22, and 8.9 K, in a magnetic field of 4.5 T MCD is predominantly due to Ni(III), which is the only paramagnetic species in the oxidized enzyme. Reproduced, with permission, from Ref. 57.

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