title: Conformational coupling between the active site and residues within the K(C)-channel of the Vibrio cholerae cbb3-type (C-family) oxygen reductase.
abstract: The respiratory chains of nearly all aerobic organisms are terminated by proton-pumping heme-copper oxygen reductases (HCOs). Previous studies have established that C-family HCOs contain a single channel for uptake from the bacterial cytoplasm of all chemical and pumped protons, and that the entrance of the K(C)-channel is a conserved glutamate in subunit III. However, the majority of the K(C)-channel is within subunit I, and the pathway from this conserved glutamate to subunit I is not evident. In the present study, molecular dynamics simulations were used to characterize a chain of water molecules leading from the cytoplasmic solution, passing the conserved glutamate in subunit III and extending into subunit I. Formation of the water chain, which controls the delivery of protons to the K(C)-channel, was found to depend on the conformation of Y241(Vc), located in subunit I at the interface with subunit III. Mutations of Y241(Vc) (to A/F/H/S) in the Vibrio cholerae cbb3 eliminate catalytic activity, but also cause perturbations that propagate over a 28-Å distance to the active site heme b3. The data suggest a linkage between residues lining the K(C)-channel and the active site of the enzyme, possibly mediated by transmembrane helix α7, which contains both Y241(Vc) and the active site cross-linked Y255(Vc), as well as two CuB histidine ligands. Other mutations of residues within or near helix α7 also perturb the active site, indicating that this helix is involved in modulation of the active site of the enzyme.
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
authors.forename: Young O
authors.initials: YO
authors.lastname: Ahn
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
authors.forename: Paween
authors.initials: P
authors.lastname: Mahinthichaichan
authors.affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; and.
authors.forename: Hyun Ju
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
authors.forename: Hanlin
authors.initials: H
authors.lastname: Ouyang
authors.affiliation: Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.
authors.forename: Daniel
authors.initials: D
authors.lastname: Kaluka
authors.affiliation: Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.
authors.forename: Syun-Ru
authors.initials: SR
authors.lastname: Yeh
authors.affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; and.
authors.forename: Davinia
authors.initials: D
authors.lastname: Arjona
authors.affiliation: Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.
authors.forename: Denis L
authors.initials: DL
authors.lastname: Rousseau
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
authors.forename: Emad
authors.initials: E
authors.lastname: Tajkhorshid
authors.affiliation: Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; and.
authors.forename: Pia
authors.initials: P
authors.lastname: Adelroth
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; r-gennis@illinois.edu.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Gennis
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D003300:Copper / Q000737:chemistry; D003593:Cytoplasm / Q000378:metabolism; D003576:Electron Transport Complex IV / Q000737:chemistry*; D006639:Histidine / Q000737:chemistry; D008024:Ligands; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D010100:Oxygen / Q000737:chemistry; D011487:Protein Conformation; D011522:Protons; D013056:Spectrophotometry, Ultraviolet; D013059:Spectrum Analysis, Raman; D014734:Vibrio cholerae / Q000201:enzymology*; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D011522:Protons; D014867:Water; D006639:Histidine; D003300:Copper; C414443:cbb3 oxidase; D003576:Electron Transport Complex IV; D010100:Oxygen
keywords: Vibrio cholerae; bioenergetics; cbb3; oxygen reductase; proton pathway