NiFe hydrogenase crystal structure

Common architecture of [NiFe] hydrogenase crystal structures... 

Interpretation of the electron density maps showed that the large subunit could not be modelled beyond His536 (Fig. 6.10), that is fifteen amino acids short of the 551 residues predicted by the nucleotide sequence (Table 6.2). At about the same time, the cleavage of this fifteen-residue stretch, which is performed by a specific protease, was reported to be an obligatory step for the maturation of the enzyme (Menon et al. 1993). It is also of interest to note that in all [NiFe] hydrogenase crystal structures this buried C-terminal histidine is ligated to a metal atom which is either a magnesium or an iron (see above). 

Figure 6.9 Common architecture of [NiFe] hydrogenase crystal structures. [FeS] clusters, metal and xenon sites are shown as spheres. Included is also an averaged internal cavity map, calculated with an accessible probe radius of 0.1 nm, of D. gigas and Dm. baculatum hydrogenase.

Heterodimeric [NiFe]-hydrogenase crystal structures have been reported for four closely related sulfate-reducing bacteria from Desulfovibrio sp. D. gi-gas [40,41], D. vulgaris (Miyazaki) [42 - 44], D. fructosovorans [45,46] and D. desulfuricans [47]. Overall, the structures are very similar being roughly... 

Nickel is found in thiolate/sulflde environment in the [NiFe]-hydrogenases and in CODH/ACS.33 In addition, either a mononuclear Ni-thiolate site or a dinuclear cysteine-S bridged structure are assumed plausible for the new class of Ni-containing superoxide dismutases, NiSOD (A).34 [NiFe]-hydrogenase catalyzes the two-electron redox chemistry of dihydrogen. Several crystal structures of [NiFe]-hydrogenases have demonstrated that the active site of the enzyme consists of a heterodinuclear Ni—Fe unit bound to thiolate sulfurs of cysteine residues with a Ni—Fe distance below 3 A (4) 35-39 This heterodinuclear active site has been the target of extensive model studies, which are summarized in Section 6.3.4.12.5. 

Many essential strnctural and functional features of hydrogenases have been derived from a wealth of various biochemical and spectroscopic methods. However, the knowledge of their atomic architectures have been obtained only very recently with the determination of the crystal structures of several hydrogenases belonging to both [NiFe] and [Fe] families (Table 6.1). These results have given a firm and nniqne strnctural basis to understand how these enzymes are actually working. 

Figure 2 Schematic view of the structure of [NiFe] hydrogenase based on the crystal structure [61,62],...

Several crystal structures of [NiFe] hydrogenases have been determined from sulfate-reducing and photosynthetic bacteria [8, 84, 85], and recently also from oxygen-tolerant species [9, 10]. Two structures from the subclass [NiFeSe] hydrogenase are known [86-88] and from two [FeFe] hydrogenases [8, 89, 90],... 

Ogata H, Kellers P, Lubitz W. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum characterization of the oxidized enzyme (Ni-A state). J Mol Biol. 2010 402(2) 428-44. 

The initial proton release associated with H2 cleavage is promoted by a base. For hydrogen evolution, net proton uptake from the medium is necessary. Conversely, for Hj oxidation protons are transferred from the active site to solution. The transfer of protons within a protein is considered to involve small (<1 ) movements of the amino acids that participate in the pathway (Williams, 1995). The proton transfer would involve a rotation of each individual donor and acceptor. Analyses of the crystal structures have suggested proton transfer pathways for the NiFe and Fe-only hydrogenases. 

X-ray crystal structures are available for cubane-type [3Fe-4S] centers in 3Fe and 7Fe Fds, aconitase, NiFe-hydrogenases, succinate dehydrogenase, fumarate... 

A major problem in the purification and crystallization of the NiFe-hydrogenases has been that they are often membrane-bound enzymes and hence it has been difficult to solubilise and hence crystallise these proteins. Thus, it is only recently that the structures of Ni-containing hydrogenases have been determined [7-14]. 

Calculations have been carried out on simplified models of the active site of [NiFe] hydrogenase in order to investigate the different active or inactive forms of the enzyme. Due to the lack of crystal structures of all the different redox states (there are at least seven that have been identified spectroscopically) of the enzyme, theoreticians have computed different possibilities for these states based on their primary spectroscopic features. Mechanistic conclusions for H2 activation processes at these sites have been made using the proposed calculated structures. 

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