title: Unification of [FeFe]-hydrogenases into three structural and functional groups.
abstract: [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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  This classification scheme provides a framework for future biochemical and mutagenesis studies to elucidate the functional role of Hyd enzymes.
authors.affiliation: Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States. Electronic address: saroz189@gmail.com.
authors.forename: Saroj
authors.initials: S
authors.lastname: Poudel
authors.affiliation: Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States. Electronic address: tokminalukas@gmail.com.
authors.forename: Monika
authors.initials: M
authors.lastname: Tokmina-Lukaszewska
authors.affiliation: Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States. Electronic address: daniel.colman@montana.edu.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Colman
authors.affiliation: Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States. Electronic address: refai1982@gmail.com.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Refai
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States. Electronic address: gerti@uga.edu.
authors.forename: Gerrit J
authors.initials: GJ
authors.lastname: Schut
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States. Electronic address: Paul.King@nrel.gov.
authors.forename: Paul W
authors.initials: PW
authors.lastname: King
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States. Electronic address: PinChing.Maness@nrel.gov.
authors.forename: Pin-Ching
authors.initials: PC
authors.lastname: Maness
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States. Electronic address: adams@bmb.uga.edu.
authors.forename: Michael W W
authors.initials: MW
authors.lastname: Adams
authors.affiliation: Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States. Electronic address: john.peters@chemistry.montana.edu.
authors.forename: John W
authors.initials: JW
authors.lastname: Peters
authors.affiliation: Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States. Electronic address: bbothner@montana.edu.
authors.forename: Brian
authors.initials: B
authors.lastname: Bothner
authors.affiliation: Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, United States. Electronic address: eboyd@montana.edu.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Boyd
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D002384:Catalysis; D020134:Catalytic Domain; D004579:Electron Transport / Q000502:physiology; D006859:Hydrogen / Q000378:metabolism; D006864:Hydrogenase / Q000378:metabolism*; D007501:Iron / Q000378:metabolism; D007506:Iron-Sulfur Proteins / Q000378:metabolism*; D010084:Oxidation-Reduction; D010766:Phosphorylation / Q000502:physiology; D011499:Protein Processing, Post-Translational / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D007506:Iron-Sulfur Proteins; D006859:Hydrogen; D007501:Iron; D006864:Hydrogenase
keywords: Bioinformatics; Electron bifurcation; Hydrogen; Post-translational modification; Regulation; [FeFe]-hydrogenase