Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases

Szőri-Dorogházi, Emma; Maróti, Gergely; Szőri, Milán; Nyilasi, Andrea; Rákhely, Gábor; Kovács, Kornél L.

doi:10.1371/journal.pone.0034666

Cited by 28 publications

(50 citation statements)

References 49 publications

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“…4A. Mutagenesis of the nearby Arg, Glu and His residues leads to loss or attenuation of catalytic activity, consistent with their proposed function in proton transfer (PT) and/or H-bonding interactions with the [NiFe] cluster [116,117]. In addition, electron nuclear double resonance (ENDOR) spectroscopy and high-resolution crystallography have shown that the Se/S groups that coordinate Ni can function as a base to accept protons during PT and H 2 activation [6].…”

Section: Hydrogenase Mechanismsupporting

confidence: 57%

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

Peters

Schut

Boyd

et al. 2015

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

398

397

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The [FeFe]- and [NiFe]-hydrogenases catalyze the formal interconversion between hydrogen and protons and electrons, possess characteristic non-protein ligands at their catalytic sites and thus share common mechanistic features. Despite the similarities between these two types of hydrogenases, they clearly have distinct evolutionary origins and likely emerged from different selective pressures. [FeFe]-hydrogenases are widely distributed in fermentative anaerobic microorganisms and likely evolved under selective pressure to couple hydrogen production to the recycling of electron carriers that accumulate during anaerobic metabolism. In contrast, many [NiFe]-hydrogenases catalyze hydrogen oxidation as part of energy metabolism and were likely key enzymes in early life and arguably represent the predecessors of modern respiratory metabolism. Although the reversible combination of protons and electrons to generate hydrogen gas is the simplest of chemical reactions, the [FeFe]- and [NiFe]-hydrogenases have distinct mechanisms and differ in the fundamental chemistry associated with proton transfer and control of electron flow that also help to define catalytic bias. A unifying feature of these enzymes is that hydrogen activation itself has been restricted to one solution involving diatomic ligands (carbon monoxide and cyanide) bound to an Fe ion. On the other hand, and quite remarkably, the biosynthetic mechanisms to produce these ligands are exclusive to each type of enzyme. Furthermore, these mechanisms represent two independent solutions to the formation of complex bioinorganic active sites for catalyzing the simplest of chemical reactions, reversible hydrogen oxidation. As such, the [FeFe]- and [NiFe]-hydrogenases are arguably the most profound case of convergent evolution. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

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Section: Hydrogenase Mechanismsupporting

confidence: 57%

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

Peters

Schut

Boyd

et al. 2015

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

398

397

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“…92 Although no data are available for AaHase, AaGlu13 L probably plays an important role, since, as stated earlier, its side-chain presents two conformations pointing either toward the proximal FeS cluster or the active site. Additionally, AaGlu13 L is listed as a MS residue, thus further supporting the hypothesis of its functional relevance.…”

Section: ■ Materials and Methodsmentioning

confidence: 94%

“…Different techniques such as spectroscopy, 18,97,98 site-directed mutagenesis, 67,92 and in silico approaches 68,69,82−84 have been used to clarify the complexity associated with this family.…”

Section: ■ Conclusionmentioning

confidence: 99%

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

et al. 2014

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[NiFe]-hydrogenases catalyze the cleavage of molecular hydrogen into protons and electrons and represent promising tools for H2-based technologies such as biofuel cells. However, many aspects of these enzymes remain to be understood, in particular how the catalytic center can be protected from irreversible inactivation by O2. In this work, we combined homology modeling, all-atom molecular dynamics, and coarse-grain Brownian dynamics simulations to investigate and compare the dynamic and mechanical properties of two [NiFe]-hydrogenases: the soluble O2-sensitive enzyme from Desulfovibrio fructosovorans, and the O2-tolerant membrane-bound hydrogenase from Aquifex aeolicus. We investigated the diffusion pathways of H2 from the enzyme surface to the central [NiFe] active site, and the possible proton pathways that are used to evacuate hydrogen after the oxidation reaction. Our results highlight common features of the two enzymes, such as a Val/Leu/Arg triad of key residues that controls ligand migration and substrate access in the vicinity of the active site, or the key role played by a Glu residue for proton transfer after hydrogen oxidation. We show specificities of each hydrogenase regarding the enzymes internal tunnel network or the proton transport pathways.

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“…Additionally, structural analysis of D. vulgaris hydrogenase has identified three possible proton transfer routes starting from this conserved glutamate [10]. A second proton transfer pathway was identified by mutagenesis of a highly-conserved, histidine-rich motif observed in many membrane bound hydrogenases [11]. Mutagenesis of His104 from D. gigas hydrogenase (His119 in E. coli) produced an enzyme with a significantly impaired activity and computational analysis identified a possible route for proton transfer independent of Glu28 but including the highly conserved Asp118 (see below) and His119 [11] .…”

Section: Hydrogenase Structure and Activitymentioning

confidence: 99%

“…The conservation of the arginine had been attributed to a role in stabilization of the structure, including a proposed hydrogen bond to one of the Fe cyanide ligands [12,13], although the geometry of this hydrogen bond is not favourable. The functional role of the arginine has not, however, been investigated by site-directed mutagenesis, although there were two unsuccessful attempts to replace the arginine with alternative side-chains in enzymes from Thiocapsa roseopersicina [11] and Desulfovibrio fructosovorans [14], which did not lead to production of mature enzyme.…”

Section: Hydrogenase Structure and Activitymentioning

confidence: 99%

Hydrogen activation by [NiFe]-hydrogenases

Carr

Evans

Brooke

et al. 2016

Biochemical Society Transactions

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Hydrogenase-1 (Hyd-1) from Escherichia coli is a membrane-bound enzyme that catalyses the reversible oxidation of molecular H2 The active site contains one Fe and one Ni atom and several conserved amino acids including an arginine (Arg(509)), which interacts with two conserved aspartate residues (Asp(118) and Asp(574)) forming an outer shell canopy over the metals. There is also a highly conserved glutamate (Glu(28)) positioned on the opposite side of the active site to the canopy. The mechanism of hydrogen activation has been dissected by site-directed mutagenesis to identify the catalytic base responsible for splitting molecular hydrogen and possible proton transfer pathways to/from the active site. Previous reported attempts to mutate residues in the canopy were unsuccessful, leading to an assumption of a purely structural role. Recent discoveries, however, suggest a catalytic requirement, for example replacing the arginine with lysine (R509K) leaves the structure virtually unchanged, but catalytic activity falls by more than 100-fold. Variants containing amino acid substitutions at either or both, aspartates retain significant activity. We now propose a new mechanism: heterolytic H2 cleavage is via a mechanism akin to that of a frustrated Lewis pair (FLP), where H2 is polarized by simultaneous binding to the metal(s) (the acid) and a nitrogen from Arg(509) (the base).

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Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases

Cited by 28 publications

References 49 publications

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Hydrogen activation by [NiFe]-hydrogenases

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