The [NiFe] and [NiFeSe] hydrogenases have remarkably similar structures, leading to the suggestion that one sulfur on a Fe-S cluster was replaced by a selenium atom, but these hydrogenases differ in catalytic reactivity and sensitivity to enzyme inhibitors.
The exact reaction mechanism of [NiFe] hydrogenases has been a matter of great debate. In 2009, a mechanism was proposed by Higuchi and coworkers based on X-ray crystallography and spectroscopic data of Desulfovibrio vulgaris Miyazaki F. During the catalytic process, the Fe ion in the active site does not change its oxidation state while the Ni metal ion participates in redox chemistry. There are two main groups of redox states that [NiFe] hydrogenases pass through during catalysis:
Ni-A (the “unready” state) and Ni-B (the “ready” state) are the most oxidized forms of the [NiFe] metal center and are activated via one-electron reduction with proton transfer. The rate of reductive activation of Ni-A to Ni-SU can take hours while the rate of reductive activation of Ni-B to Ni-SIr happens in seconds. The reason for this disparity in activation kinetics between Ni-A and Ni-B was proposed to be a result of the difference in bridging ligands between the two different redox states. At the Ni-SIr state, a water molecule was released to form the Ni-SIa state, the first catalytic redox active state of [NiFe] hydrogenases.
The three most important catalytic redox active states of [NiFe] hydrogenases are Ni-SIa, Ni-C and Ni-R (which have three different variations). The light-sensitive Ni-C state can be obtained via one electron reduction of Ni-SIa. The electron paramagnetic resonance spectroscopic studies of the Ni-C state, which contained a Ni3+ with S = 1/2 and a hydride bridging the two metals, Ni and Fe, showed that the heterolytic cleavage of H2 takes place in the [NiFe] hydrogenase active site.
Ni-SIa state can be inhibited by CO, which binds directly to Ni metal ion in a bent conformation to form Ni-SCO (see below). Since Ni-C is light sensitive, illumination at 100 K results in Ni-L redox state. During this process, nickel is reduced. In the presence of CO, Ni-L forms Ni-CO state.
The maturation of [NiFe] hydrogenases requires a set of accessory proteins that synthesize the NiFe active site and modify the precursor enzyme so that it has the correct structure and location. The maturation of the active site is of special interest because of the synthesis of cyanide (CN) and carbon monoxide (CO) metal ligands which are usually toxic to living organism. This step is completed by the proteins HypC, HypD, HypE, and HypF. After, synthesis of the iron center, nickel is inserted using metallochaperones HypA, HypB, and SlyD. Once the catalytic center is completed, the hydrogenase precursor undergoes a C-terminal cleavage that prompts rearrangement of its structure and association with the small subunit. Finally, the completed enzyme is transported to its correct position within the cell. Hydrogenase promoter, PSH, can be studied constructing a PSH promoter-gfp fusion by using green fluorescent protein (gfp) reporter gene.
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Eidsness, M. K.; Scott, R. A.; Prickril, B. C.; DerVartanian, D. V.; Legall, J.; Moura, I.; Moura, J. J.; Peck, H. D. (1989). "Evidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus". Proceedings of the National Academy of Sciences. 86 (1): 147–151. doi:10.1073/pnas.86.1.147. PMC 286421. PMID 2521386. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC286421
Ogata, H.; Lubitz, W.; Higuchi, Y. (2009). "[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism". Dalton Trans. 37 (37): 7577–7587. doi:10.1039/b903840j. PMID 19759926. /wiki/Doi_(identifier)
Ogata, H.; Lubitz, W.; Higuchi, Y. (2009). "[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism". Dalton Trans. 37 (37): 7577–7587. doi:10.1039/b903840j. PMID 19759926. /wiki/Doi_(identifier)
Ogata, H.; Lubitz, W.; Higuchi, Y. (2009). "[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism". Dalton Trans. 37 (37): 7577–7587. doi:10.1039/b903840j. PMID 19759926. /wiki/Doi_(identifier)
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Lamele, S. E.; Albracht, S. P. J.; Armstrong, F. A. (2004). "Electrochemical Potential-Step Investigations of the Aerobic Interconversions of [NiFe]-Hydrogenase from Allochromatium vinosum: Insights into the Puzzling Difference between Unready and Ready Oxidized Inactive States". Journal of the American Chemical Society. 126 (45): 14899–14909. doi:10.1021/ja047939v. PMID 15535717. /wiki/Doi_(identifier)
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Ogata, H.; Mizoguchi, Y.; Mizuno, N.; Miki, K.; Adachi, S.-i.; Yasuoka, N.; Yagi, T.; Yamauchi, O.; Hirota, S.; Higuchi, Y. (2002). "Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen". Journal of the American Chemical Society. 124 (39): 11628–11635. doi:10.1021/ja012645k. PMID 12296727. /wiki/Doi_(identifier)
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Lacasse, Michael J.; Zamble, Deborah B. (29 March 2016). "[NiFe]-Hydrogenase Maturation". Biochemistry. 55 (12): 1689–1701. doi:10.1021/acs.biochem.5b01328. PMID 26919691. /wiki/Deborah_Zamble
Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.; Mulder, David W.; Shepard, Eric M.; Broderick, Joan B.; King, Paul W.; Adams, Michael W.W. (June 2015). "[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1853 (6): 1350–1369. doi:10.1016/j.bbamcr.2014.11.021. PMID 25461840. https://scholarworks.montana.edu/bitstreams/b2a80673-d5a2-4dfe-8427-ce38888b2fb5/download
Lubitz, Wolfgang; Ogata, Hideaki; Rüdiger, Olaf; Reijerse, Edward (23 April 2014). "Hydrogenases". Chemical Reviews. 114 (8): 4081–4148. doi:10.1021/cr4005814. PMID 24655035. /wiki/Wolfgang_Lubitz
Lacasse, Michael J.; Zamble, Deborah B. (29 March 2016). "[NiFe]-Hydrogenase Maturation". Biochemistry. 55 (12): 1689–1701. doi:10.1021/acs.biochem.5b01328. PMID 26919691. /wiki/Deborah_Zamble
Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.; Mulder, David W.; Shepard, Eric M.; Broderick, Joan B.; King, Paul W.; Adams, Michael W.W. (June 2015). "[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1853 (6): 1350–1369. doi:10.1016/j.bbamcr.2014.11.021. PMID 25461840. https://scholarworks.montana.edu/bitstreams/b2a80673-d5a2-4dfe-8427-ce38888b2fb5/download
Lubitz, Wolfgang; Ogata, Hideaki; Rüdiger, Olaf; Reijerse, Edward (23 April 2014). "Hydrogenases". Chemical Reviews. 114 (8): 4081–4148. doi:10.1021/cr4005814. PMID 24655035. /wiki/Wolfgang_Lubitz
Lacasse, Michael J.; Zamble, Deborah B. (29 March 2016). "[NiFe]-Hydrogenase Maturation". Biochemistry. 55 (12): 1689–1701. doi:10.1021/acs.biochem.5b01328. PMID 26919691. /wiki/Deborah_Zamble
Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.; Mulder, David W.; Shepard, Eric M.; Broderick, Joan B.; King, Paul W.; Adams, Michael W.W. (June 2015). "[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1853 (6): 1350–1369. doi:10.1016/j.bbamcr.2014.11.021. PMID 25461840. https://scholarworks.montana.edu/bitstreams/b2a80673-d5a2-4dfe-8427-ce38888b2fb5/download
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