A Water Dimer Shift Activates a Proton Pumping Pathway in the PR ? F Transition of ba3 Cytochrome c Oxidase.

ABSTRACT: Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR ? F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+?O2-···CuB2+, in which the H2O ligand that resulted from protonation of the OH- ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+?O2- distance in F (1.68 Å) is 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+?O2- stretching modes in P (804 cm-1) and F (785 cm-1) identified by resonance Raman experiments. In this F state, the CuB2+···O2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent OH state [Fea33+-OH--CuB2+] with a ?-hydroxo bridge can be easily formed, as shown by our calculations.

SUBMITTER: Han Du WG 

PROVIDER: S-EPMC5825212 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature