Conformational Flexibility of D1-Glu189: A Crucial Determinant in Substrate Water Selection, Positioning, and Stabilization within the Oxygen-Evolving Complex of Photosystem II

Abstract

Photosynthetic water oxidation is a vital process responsible for producing dioxygen and supplying the energy necessary to sustain life on Earth. This fundamental reaction is catalyzed by the oxygen-evolving complex (OEC) of photosystem II, which houses the Mn₄CaO₅ cluster as its catalytic core. In this study, we specifically focus on the D1-Glu189 amino acid residue, which serves as a direct ligand to the Mn₄CaO₅ cluster. Our primary goal is to explore, using density functional theory (DFT), how the conformational flexibility of the D1-Glu189 side chain influences crucial catalytic processes, particularly the selection, positioning, and stabilization of a substrate water molecule within the OEC. Our investigation is based on a hypothesis put forth by Li et al. (Nature, 2024, 626, 670), which suggests that during the transition from the S₂ to S₃ state, a specific water molecule temporarily coordinating with the Ca ion, referred to as O6*, may exist as a hydroxide ion (OH^-). Our results demonstrate a key mechanism by which the detachment of the D1-Glu189 carboxylate group from its coordination with the Ca ion allows the creation of a specialized microenvironment within the OEC that enables the selective attraction of O6* in its deprotonated form (OH^-) and stabilizes it at the catalytic metal (Mn_D) site. Our findings indicate that D1-Glu189 is not only a structural ligand for the Ca ion but may also play an active and dynamic role in the catalytic process, positioning O6* optimally for its subsequent participation in the oxidation sequence during the water-splitting cycle.

Figure 1

Conformational changes of amino acid residues within the primary coordination sphere of the Mn cluster observed experimentally during the S₂ to S₃ transition. Structural models captured at 1F (red), and time points at 20 ns (gray), 200 ns (orange), 1 μs (light green), 30 μs (pink), 200 μs (cyan), and 5 ms (gold) after 2F are superimposed. The inorganic Mn₄CaO₅ cluster is displayed in wireframe, while seven amino acid residues in the primary coordination sphere are shown in stick representation.

Figure 2

A potential energy surface representing the energy change (ΔE) as a function of the dihedral angles D₂ and D₃ of D1-Glu189. These calculations were based on the PDB coordinates (6JLL, monomer A), with an additional O6* remaining attached to the Ca ion of the Mn cluster. The relative energy ΔE is referenced to the metastable structure depicted in Figure S1B. White circles indicate the D₂ and D₃ values corresponding to the motion of the D1-Glu189 side chain when coupled with O6* binding to Mn_D (see Figure 3). A magenta circle represents the D₂ and D₃ values observed in the S₃ state, in which O5 and O6 either form an oxyl-oxo bond or exist as bridging oxo and terminal hydroxo ligands.

Figure 3

(A) Conformational changes in the side chain of D1-Glu189 as O6* moves toward Mn_D. The colors of O6* and D1-Glu189 correspond to the relative energy (ΔE) compared to the metastable structure shown in Figure S1B. (B) Conformational changes in the side chain of D1-Glu189 as O6* (renamed O6) binds to Mn_D, followed by the return of D1-Glu189 to its original orientation. The experimentally observed conformation in the S₃ state (6JLL, monomer A) is highlighted in magenta. (C, D) A sphere representation illustrates Ca and the coordinating oxygen atoms of D1-Glu189 during O6* binding to Mn_D, aiding in the comprehension of the steric hindrance resulting from repulsive forces between neighboring Ca, D1-Glu189, and moving O6*. (E) Fluctuations of five water molecules (W10, W20, W21, W22, and W23) accompanying the movement of O6* toward Mn_D. Purple dashed lines represent hydrogen bonds between O6* and W21, as well as between O6* and W10, contributing to the stabilization of the anionic form of O6* (OH^–). As O6* moves closer to Mn_D, W21 is also pulled toward the space between Ca and D1-Glu189 due to its interaction with O6*, while interference from D1-Glu189 (not shown) causes the hydrogen bond between O6* and W10 to break just before O6* binds to Mn_D (O6* → O6).

Figure 4

A proposed reaction mechanism for the S₂ to S₃ transition, based on the high-valent scheme.