9W5B

cryo-EM structure of PSII D1-S264V from Thermosynechococcus vestitus BP-1

Summary for 9W5B

• Entry DOI: 10.2210/pdb9w5b/pdb
• EMDB information: 65652
• Descriptor: Photosystem II protein D1 3, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (38 entities in total)
• Functional Keywords: psii mutation, photosynthesis
• Biological source: Thermosynechococcus vestitus BP-1; More
• Total number of polymer chains: 38
• Total formula weight: 735626.80

Authors

Fan, S.B.,Jiang, H.W.,Kato, K.,Tsai, P.-C.,Jia, A.Q.,Nakajima, Y.,Sugiura, M.,Shen, J.-R. (deposition date: 2025-08-01, release date: 2026-09-23)

Primary citation

Fan, S.,Nakajima, Y.,Kato, K.,Jiang, H.,Tsai, P.C.,Jia, A.,Sugiura, M.,Shen, J.R.
Structural and functional analysis of a photosystem II mutant PsbA3-S264V.
Biochim Biophys Acta Bioenerg, 1868:149607-149607, 2026

PubMed Abstract: Photosystem II (PSII) catalyzes water oxidation and oxygen evolution by a light-induced electron transfer chain, leading to the generation of electrons, protons and dioxygen. D1-S264 is a residue located close to the Q-binding site, and mutation of this residue has been shown to bring significant effects on the electron transfer and oxygen-evolving activities. Here we analyzed the structure of a Thermosynechococcus elongatus mutant PsbA3-S264V by cryo-electron microscopy at 1.96 Å resolution, which showed significant changes in the structure surrounding the bicarbonate and Q-binding region. Due to change of Ser to Val, the hydrogen-bond between the Q carbonyl oxygen and S264 is altered, which changed the protonation pathway of Q from the original route of D1-H252 through D1-S264 to Q, to a new, longer and less efficient route of D1-H252 through D1-F265 to Q. Two residues, D1-E244 and D2-E242, changed their side chain orientations significantly. Among them, D2-E242 adopted two conformations, and both are largely deviated from the original structure. All these changes led to alterations in hydrogen-bonding networks of two channels, channel A and channel B, that connect the stromal surface to Q and may function to transport protons to protonate Q. Furthermore, isothermal titration calorimetry experiments showed a diminished 3-(3,4-dichlorophenyl)-1, 1-dimethylurea (DCMU) binding affinity of the mutated PSII, which may be explained by a structural rotation of D1-F255 in the mutant based on structural analysis of DCMU-bound PSII. These findings offer valuable insights into the functions of D1-S264 in Q protonation and function, as well as in the DCMU-binding.

PubMed: 42702229
DOI: 10.1016/j.bbabio.2026.149607

Experimental method

ELECTRON MICROSCOPY (1.96 Å)