Unification of [FeFe]-Hydrogenases into Three Structural and Functional Groups

Paul King, Pin-Ching Maness, Saroj Poudela, Monika Tokmina-Lukaszewska, Daniel Colman, Mohammed Refai, Gerrit Schut, Michael Adams, John Peters, Brian Bothner, Eric Boyd

Research output: Contribution to journalArticlepeer-review

53 Scopus Citations

Abstract

Background [FeFe]-hydrogenases (Hyd) are structurally diverse enzymes that catalyze the reversible oxidation of hydrogen (H2). 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 H2. Methods 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, and regulatory proteins encoded in HydA gene neighborhoods. Results 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 suggest that they are post-translationally modified by phosphorylation. Conclusions 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. General significance This classification scheme provides a framework for future biochemical and mutagenesis studies to elucidate the functional role of Hyd enzymes.

Original languageAmerican English
Pages (from-to)1910-1921
Number of pages12
JournalBiochimica et Biophysica Acta - General Subjects
Volume1860
Issue number9
DOIs
StatePublished - 1 Sep 2016

Bibliographical note

Publisher Copyright:
© 2016 Elsevier B.V. All rights reserved.

NREL Publication Number

  • NREL/JA-2700-66632

Keywords

  • Bioinformatics
  • Electron bifurcation
  • Hydrogen
  • Post-translational modification
  • Regulation
  • [FeFe]-hydrogenase

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