5G38

PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 6

Summary for 5G38

• Entry DOI: 10.2210/pdb5g38/pdb
• Related: 5G39 5G3A
• Descriptor: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, CALCIUM ION (3 entities in total)
• Functional Keywords: photosynthesis, carboxylate cluster, ph, proton antenna
• Biological source: THERMOSYNECHOCOCCUS ELONGATUS
• Total number of polymer chains: 1
• Total formula weight: 18741.96

Authors

Bommer, M.,Bondar, A.N.,Zouni, A.,Dobbek, H.,Dau, H. (deposition date: 2016-04-24, release date: 2016-08-10, Last modification date: 2024-10-23)

Primary citation

Bommer, M.,Bondar, A.N.,Zouni, A.,Dobbek, H.,Dau, H.
Crystallographic and Computational Analysis of the Barrel Part of the Psbo Protein of Photosystem II -Carboxylate-Water Clusters as Putative Proton Transfer Relays and Structural Switches
Biochemistry, 55:4626-, 2016

PubMed Abstract: In all organisms that employ oxygenic photosynthesis, the membrane-extrinsic PsbO protein is a functionally important component of photosystem II. To study the previously proposed proton antenna function of carboxylate clusters at the protein-water interface, we combined crystallography and simulations of a truncated cyanobacterial (Thermosynechococcus elongatus) PsbO without peripheral loops. We expressed the PsbO β-barrel heterologously and determined crystal structures at resolutions of 1.15-1.5 Å at 100 K at various pH values and at 297 K and pH 6. (1) Approximately half of the 177 surface waters identified at 100 K are resolved at 297 K, suggesting significant occupancy of specific water sites at room temperature, and loss of resolvable occupancy for other sites. (2) Within a loop region specific to cyanobacterial PsbO, three residues and four waters coordinating a calcium ion are well ordered even at 297 K; the ligation differs for manganese. (3) The crystal structures show water-carboxylate clusters that could facilitate fast Grotthus-type proton transfer along the protein surface and/or store protons. (4) Two carboxylate side chains, which are part of a structural motif interrupting two β-strands and connecting PsbO to photosystem II, are within hydrogen bonding distance at pH 6 (100 K). Simulations indicate coupling between protein structure and carboxylate protonation. The crystal structure determined at 100 K and pH 10 indicates broken hydrogen bonding between the carboxylates and local structural change. At pH 6 and 297 K, both conformations were present in the crystal, suggesting conformational dynamics in the functionally relevant pH regime. Taken together, crystallography and molecular dynamics underline a possible mechanism for pH-dependent structural switching.

PubMed: 27454911
DOI: 10.1021/ACS.BIOCHEM.6B00441

Experimental method

X-RAY DIFFRACTION (1.15 Å)