9EH5

Structure of a mutated photosystem II complex reveals changes to the hydrogen-bonding network that affect proton egress during O-O bond formation

Summary for 9EH5

• Entry DOI: 10.2210/pdb9eh5/pdb
• EMDB information: 48046
• Descriptor: Photosystem II protein D1 2, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (38 entities in total)
• Functional Keywords: photosynthesis, photosystem ii, oxygen-evolving complex, transition metals, metalloenzyme, mutagenesis, water channel, hydrogen-bond network
• Biological source: Synechocystis sp. PCC 6803; More
• Total number of polymer chains: 42
• Total formula weight: 816308.45

Authors

Flesher, D.A.,Shin, J.,Debus, R.J.,Brudvig, G.W. (deposition date: 2024-11-22, release date: 2025-02-19)

Primary citation

Flesher, D.A.,Shin, J.,Debus, R.J.,Brudvig, G.W.
Structure of a mutated photosystem II complex reveals changes to the hydrogen-bonding network that affect proton egress during O-O bond formation.
J.Biol.Chem., :108272-108272, 2025

PubMed Abstract: Photosystem II (PSII) is the water-splitting enzyme of oxygenic photosynthesis. Using light energy, PSII catalytically oxidizes two water molecules to fuel downstream metabolism, forming an O-O bond and releasing O as a byproduct. The reaction mechanism requires the strategic removal of four protons via conserved hydrogen-bonding networks, but these pathways remain poorly understood. Site-directed mutagenesis has been used to study these pathways and the role of specific side chains, such as Lys317 of the D2 subunit. Previous studies showed that the D2-Lys317Ala substitution, which abolishes the flexible hydrogen-bonding -NH group, resulted in delayed O release kinetics and diminished catalytic turnover, suggesting Lys317 has a crucial role in facilitating proton egress. Here, we investigated this proton egress pathway by determining the cryo-EM structure of PSII containing the D2-Lys317Ala substitution at a resolution of 1.97 Å. We observed that four new water molecules fill the space previously occupied by Lys317, but these waters lack specific water-protein interactions, leading to heterogeneity and suboptimal hydrogen bonding. We hypothesize that these waters negatively contribute to the existing hydrogen-bonding network and increase the entropic barrier for proton transfer. Additionally, we observed that a conserved chloride ion (Cl1), which is associated with Lys317, is unexpectedly maintained in D2-Lys317Ala PSII. However, unlike in wild-type, Cl1 has no measured effect on oxygen-evolution rates in D2-Lys317Ala PSII. This suggests that the role of Cl1 is dependent on the Lys317 amino group. These findings provide new insight into proton egress through the Cl1 hydrogen-bonding channel.

PubMed: 39922494
DOI: 10.1016/j.jbc.2025.108272

Experimental method

ELECTRON MICROSCOPY (1.97 Å)