O2 evolution and recovery of the water-oxidizing enzyme.

In photosystem II, light-induced water oxidation occurs at the Mn4CaO5 cluster. Here we demonstrate proton releases, dioxygen formation, and substrate water incorporation in response to Mn4CaO5 oxidation in the protein environment, using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. In S2, H2O at the W1 site forms a low-barrier H-bond with D1-Asp61. In the S2-to-S3 transition, oxidation of OW1H- to OW1•-, concerted proton transfer from OW1H- to D1-Asp61, and binding of a water molecule Wn-W1 at OW1•- are observed. In S4, W n-W1 facilitates oxo-oxyl radical coupling between OW1•- and corner µ-oxo O4. Deprotonation via D1-Asp61 leads to formation of OW1=O4. As OW1=O4 moves away from Mn, H2O at W539 is incorporated into the vacant O4 site of the O2-evolved Mn4CaO4 cluster, forming a µ-oxo bridge (Mn3-OW539-Mn4) in an exergonic process. Simultaneously, Wn-W1 is incorporated as W1, recovering the Mn4CaO5 cluster.

pK a of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution.

Quinones can accept two electrons and two protons, and are involved in electron transfer and proton transfer reactions in photosynthetic reaction centers. To date, the pK a of these quinones in aqueous solution have not been reported. We calculated the pK a of the initial protonation (Q·- to QH·) and the second protonation (QH- to QH2) of 1,4-quinones using a quantum chemical approach. The calculated energy differences of the protonation reactions Q·- to QH· and QH- to QH2 in the aqueous phase for nine 1,4-quinones were highly correlated with the experimentally measured pK a(Q·-/QH·) and pK a(QH-/QH2), respectively. In the present study, we report the pK a(Q·-/QH·) and pK a(QH-/QH2) of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution.

A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase.

The biosynthesis of isopentenyl diphosphate, a fundamental precursor for isoprenoids, via the mevalonate pathway is completed by diphosphomevalonate decarboxylase. This enzyme catalyzes the formation of isopentenyl diphosphate through the ATP-dependent phosphorylation of the 3-hydroxyl group of (R)-5-diphosphomevalonate followed by decarboxylation coupled with the elimination of the 3-phosphate group. In this reaction, a conserved aspartate residue has been proposed to be involved in the phosphorylation step as the general base catalyst that abstracts a proton from the 3-hydroxyl group. In this study, the catalytic mechanism of this rare type of decarboxylase is re-investigated by structural and mutagenic studies on the enzyme from a thermoacidophilic archaeon Sulfolobus solfataricus The crystal structures of the archaeal enzyme in complex with (R)-5-diphosphomevalonate and adenosine 5'-O-(3-thio)triphosphate or with (R)-5-diphosphomevalonate and ADP are newly solved, and theoretical analysis based on the structure suggests the inability of proton abstraction by the conserved aspartate residue, Asp-281. Site-directed mutagenesis on Asp-281 creates mutants that only show diphosphomevalonate 3-kinase activity, demonstrating that the residue is required in the process of phosphate elimination/decarboxylation, rather than in the preceding phosphorylation step. These results enable discussion of the catalytic roles of the aspartate residue and provide clear proof of the involvement of a long predicted intermediate, (R)-3-phospho-5-diphosphomevalonate, in the reaction of the enzyme.

pK(a) of a Proton-Conducting Water Chain in Photosystem II.

Recent high-resolution crystal structures of the water-oxidizing enzyme photosystem II (PSII) show that O4 of the catalytic Mn4CaO5 cluster forms an H-bond with a water molecule W539, which belongs to a chain of water molecules (O4-water chain). Oxidation of Mn4CaO5 to S1 resulted in elongation of the O-H bonds and decrease in pKa(O-H/O(-)) in the [O4-H···OW539-H···OW538-H···OW393] region along the O4-water chain. In S1, removal of all water molecules from the O4-water chain, except W539, resulted in a significant pKa upshift at O4; this suggests that the proton-conducting water chain serves as a conducting media for protons and significantly decreases the donor pKa, leading to a downhill proton transfer. The absence of a corresponding proton-conducting channel is disadvantageous for release of protons from the proton-releasing site, as in the case of O5 that has no H-bond partner.