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Title: Unification of [FeFe]-hydrogenases into three structural and functional groups

Authors:
; ; ; ; ; ORCiD logo; ; ; ; ; ORCiD logo
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Biological Electron Transfer and Catalysis (BETCy)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1388012
DOE Contract Number:
SC0012518
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochimica et Biophysica Acta - General Subjects; Journal Volume: 1860; Journal Issue: 9; Related Information: BETCy partners with Montana State University (lead); Arizona State University; National Renewable Energy Laboratory; University of Georgia; University of Kentucky; University of Washington; Utah State University
Country of Publication:
United States
Language:
English
Subject:
solar (fuels), biofuels (including algae and biomass), bio-inspired, hydrogen and fuel cells

Citation Formats

Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Refai, Mohammed, Schut, Gerrit J., King, Paul W., Maness, Pin-Ching, Adams, Michael W. W., Peters, John W., Bothner, Brian, and Boyd, Eric S. Unification of [FeFe]-hydrogenases into three structural and functional groups. United States: N. p., 2016. Web. doi:10.1016/j.bbagen.2016.05.034.
Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Refai, Mohammed, Schut, Gerrit J., King, Paul W., Maness, Pin-Ching, Adams, Michael W. W., Peters, John W., Bothner, Brian, & Boyd, Eric S. Unification of [FeFe]-hydrogenases into three structural and functional groups. United States. doi:10.1016/j.bbagen.2016.05.034.
Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Refai, Mohammed, Schut, Gerrit J., King, Paul W., Maness, Pin-Ching, Adams, Michael W. W., Peters, John W., Bothner, Brian, and Boyd, Eric S. 2016. "Unification of [FeFe]-hydrogenases into three structural and functional groups". United States. doi:10.1016/j.bbagen.2016.05.034.
@article{osti_1388012,
title = {Unification of [FeFe]-hydrogenases into three structural and functional groups},
author = {Poudel, Saroj and Tokmina-Lukaszewska, Monika and Colman, Daniel R. and Refai, Mohammed and Schut, Gerrit J. and King, Paul W. and Maness, Pin-Ching and Adams, Michael W. W. and Peters, John W. and Bothner, Brian and Boyd, Eric S.},
abstractNote = {},
doi = {10.1016/j.bbagen.2016.05.034},
journal = {Biochimica et Biophysica Acta - General Subjects},
number = 9,
volume = 1860,
place = {United States},
year = 2016,
month = 9
}
  • [FeFe]-hydrogenases (Hyd) are structurally diverse enzymes that catalyze the reversible oxidation of hydrogen (H 2). Recent biochemical data demonstrate new functional roles for these enzymes, including those that function in electron bifurcation where an exergonic reaction is coupled with an endergonic reaction to drive the reversible oxidation/production of H 2. To identify the structural determinants that underpin differences in enzyme functionality, a total of 714 homologous sequences of the catalytic subunit, HydA, were compiled. Bioinformatics approaches informed by biochemical data were then used to characterize differences in inferred quaternary structure, HydA active site protein environment, accessory iron-sulfur clusters in HydA,more » and regulatory proteins encoded in HydA gene neighborhoods. HydA homologs were clustered into one of three classification groups, Group 1 (G1), Group 2 (G2), and Group 3 (G3). G1 enzymes were predicted to be monomeric while those in G2 and G3 were predicted to be multimeric and include HydB, HydC (G2/G3) and HydD (G3) subunits. Variation in the HydA active site and accessory iron-sulfur clusters did not vary by group type. Group-specific regulatory genes were identified in the gene neighborhoods of both G2 and G3 Hyd. Analyses of purified G2 and G3 enzymes by mass spectrometry strongly suggests that they are post-translationally modified by phosphorylation. In conclusion, these results suggest that bifurcation capability is dictated primarily by the presence of both HydB and HydC in Hyd complexes, rather than by variation in HydA.« less
  • We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S]{sup +,2+}Cys{sub 4}, [4Fe4S]{sup +,2+}Cys{sub 3}His, and [2Fe2S]{sup +,2+}Cys{sub 4}, were calculated solely from Kohn-Sham density functional theory and Natural Population Analysis. Circumsphere analysis of the cubane clusters in the energy-minimized structure of the full Clostridium pasteurianum hydrogenase I showed the resulting metallocluster structures to be similar to known cubane structures. All clusters were additionally stable in molecular dynamics simulations over the course of 1.0 nsmore » in the fully oxidized and fully reduced enzyme models. Normal modes calculated by quasiharmonic analysis from the dynamics data show unexpected couplings among internal coordinate motions, which may reflect the effects of the protein structure on metallocluster dynamics.« less
  • Here, the first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogenmore » production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro, with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.« less
  • Single-walled carbon nanotubes (SWNT) are promising candidates for use in energy conversion devices as an active photo-collecting elements, for dissociation of bound excitons and charge-transfer from photo-excited chromophores, or as molecular wires to transport charge. Hydrogenases are enzymes that efficiently catalyze the reduction of protons from a variety of electron donors to produce molecular hydrogen. Hydrogenases together with SWNT suggest a novel biohybrid material for direct conversion of sunlight into H{sub 2}. Here, we report changes in SWNT optical properties upon addition of recombinant [FeFe] hydrogenases from Clostridium acetobutylicum and Chlamydomonas reinhardtii. We find evidence that novel and stable charge-transfermore » complexes are formed under conditions of the hydrogenase catalytic turnover, providing spectroscopic handles for further study and application of this hybrid system.« less