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... 

The interaction of the partially reduced Ni-C form with the [4Fe4S] proximal cluster has been studied in D. gigas hydrogenase (103). From these studies it has been possible to predict the distance between the two redox centers. The value agrees well with that observed in the crystal structure (Fig. 9). In the readily available as-... 

The 3D crystal structure of Dsm. baculatum [NiSeFe] hydrogenase has been solved 185), and it was indicated that the enzyme contains three [4Fe-4S] centers. A cysteine (replacing a proline usually found near the [3Fe-4S] core) provides an extra ligand, enabling the acceptance of a fourth iron site at this cluster. 

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. 

A template synthesis employing Ni(OAc)2, 2,5-dihydroxy-2,5-dimethyl-1,4-dithiane, and 3,3 -iminobis(propylamine) gave the water-soluble five-coordinate complex [Ni(495)], the crystal structure of which shows trigonal bipyramidal coordination of Ni11 with the central amine and terminal thiolates in plane and the two imino nitrogens in axial positions. Solvatochromism of the complex is interpreted in terms of S" H bonding, which may be of relevance to the catalytic cycle in hydrogenases.1341... 

JW. Peters, WN. Lanzilotta, BJ. Lemon, LC. eefeldt (1998) X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 Angstrom resolution. Science, 282 1853-1858... 

Figure 4.3 X-ray crystal structure of HybD, the specific protease for hydrogenase 2. 

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. 

Fritsche, E., Paschos, A., Beisel, H. G., Bock, A. and Hubeg R. (1999) Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli. J. Mol. Biol., 288,... 

Garcin, E., Vemede, X., Hatchikian, E. C., Volbeda, A., Frey, M. and Fontecilla-Camps, J. C. (1999) The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catal) tic center. Structure Fold. Des., 7, 557-66. 

Volbeda A, Charon M-H, Piras C, et al. 1995. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature 373 580-7. 

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