Photosystem II — Details of Cofactor-Protein Interactions in the Light of the 3 Å Resolution Crystal Structure

The Mn4CaO5 cluster site in the oxygen-evolving complex (OEC) of photosystem II (PSII) undergoes structural perturbations, such as those induced by Ca2+/Sr2+ exchanges or Ca/Mn removal. These changes have been known to induce long-range positive shifts (between +30 and +150 mV) in the redox potential of the primary quinone electron acceptor plastoquinone A (QA), which is located 40 Å from the OEC. To further investigate these effects, we reanalyzed the crystal structure of Sr-PSII resolved at 2.1 Å and compared it with the native Ca-PSII resolved at 1.9 Å. Here, we focus on the acceptor site and report the possible long-range interactions between the donor, Mn4Ca(Sr)O5 cluster, and acceptor sites.

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Crystal structure of the PsbQ protein of photosystem II from higher plants

EMBO Reports ◽

10.1038/sj.embor.embor923 ◽

2003 ◽

Vol 4 (9) ◽

pp. 900-905 ◽

Cited By ~ 59

Author(s):

Vito Calderone ◽

Michela Trabucco ◽

Andreja Vujičić ◽

Roberto Battistutta ◽

Giorgio Mario Giacometti ◽

...

Keyword(s):

Crystal Structure ◽

Photosystem Ii ◽

Higher Plants

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Mass spectrometry-based cross-linking study shows that the Psb28 protein binds to cytochrome b559 in Photosystem II

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1620360114 ◽

2017 ◽

Vol 114 (9) ◽

pp. 2224-2229 ◽

Cited By ~ 18

Author(s):

Daniel A. Weisz ◽

Haijun Liu ◽

Hao Zhang ◽

Sundarapandian Thangapandian ◽

Emad Tajkhorshid ◽

...

Keyword(s):

Mass Spectrometry ◽

Photosystem Ii ◽

Protein Interactions ◽

Protein Complexes ◽

Protein Docking ◽

Cross Linking ◽

Protein Protein Interactions ◽

Cytochrome B559 ◽

Reaction Center Complex ◽

Assembly Intermediate

Photosystem II (PSII), a large pigment protein complex, undergoes rapid turnover under natural conditions. During assembly of PSII, oxidative damage to vulnerable assembly intermediate complexes must be prevented. Psb28, the only cytoplasmic extrinsic protein in PSII, protects the RC47 assembly intermediate of PSII and assists its efficient conversion into functional PSII. Its role is particularly important under stress conditions when PSII damage occurs frequently. Psb28 is not found, however, in any PSII crystal structure, and its structural location has remained unknown. In this study, we used chemical cross-linking combined with mass spectrometry to capture the transient interaction of Psb28 with PSII. We detected three cross-links between Psb28 and the α- and β-subunits of cytochrome b559, an essential component of the PSII reaction-center complex. These distance restraints enable us to position Psb28 on the cytosolic surface of PSII directly above cytochrome b559, in close proximity to the QB site. Protein–protein docking results also support Psb28 binding in this region. Determination of the Psb28 binding site and other biochemical evidence allow us to propose a mechanism by which Psb28 exerts its protective effect on the RC47 intermediate. This study also shows that isotope-encoded cross-linking with the “mass tags” selection criteria allows confident identification of more cross-linked peptides in PSII than has been previously reported. This approach thus holds promise to identify other transient protein–protein interactions in membrane protein complexes.

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Crystal structure of photosystem II at 3.2 Å provides new details of protein–cofactor interactions

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767304097156 ◽

2004 ◽

Vol 60 (a1) ◽

pp. s144-s144

Author(s):

J. Biesiadka ◽

B. Loll ◽

J. Kern ◽

K.-D. Irrgang ◽

A. Zouni ◽

...

Keyword(s):

Crystal Structure ◽

Photosystem Ii

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Structural studies of the phosphatidylinositol 3-kinase (PI3K) SH3 domain in complex with a peptide ligand: role of the anchor residue in ligand binding

Biological Chemistry ◽

10.1515/bc.2010.003 ◽

2010 ◽

Vol 391 (1) ◽

Cited By ~ 14

Author(s):

Renu Batra-Safferling ◽

Joachim Granzin ◽

Susanne Mödder ◽

Silke Hoffmann ◽

Dieter Willbold

Keyword(s):

Crystal Structure ◽

Ligand Binding ◽

Protein Interactions ◽

Intracellular Signaling ◽

Sh3 Domain ◽

Peptide Ligand ◽

Type I ◽

Phosphatidylinositol 3 Kinase ◽

Anchor Residue ◽

Phosphatidylinositol 3

Abstract Src homology 3 (SH3) domains are mediators of protein-protein interactions. They comprise approximately 60 amino acid residues and are found in many intracellular signaling proteins. Here, we present the crystal structure of the SH3 domain from phosphatidylinositol 3-kinase (PI3K) in complex with the 12-residue proline-rich peptide PD1R (HSKRPLPPLPSL). The crystal structure of the PI3K SH3-PD1R complex at a resolution of 1.7 Å reveals type I ligand orientation of the bound peptide with an extended conformation where the central portion forms a left-handed type II polyproline (PPII) helix. The overall structure of the SH3 domain shows minimal changes on ligand binding. In addition, we also attempted crystallization with another peptide ligand (PD1) where the residue at anchor position P-3 is a tyrosine. The crystals obtained did not contain the PD1 ligand; instead, the ligand binding site is partially occupied by residues Arg18 and Trp55 from the symmetry-related PI3K SH3 molecule. Considering these crystal structures of PI3K SH3 together with published reports, we provide a comparative analysis of protein-ligand interactions that has helped us identify the individual residues which play an important role in defining target specificity.

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Short Hydrogen Bond between Redox-Active Tyrosine YZand D1-His190 in the Photosystem II Crystal Structure

Biochemistry ◽

10.1021/bi201366j ◽

2011 ◽

Vol 50 (45) ◽

pp. 9836-9844 ◽

Cited By ~ 78

Author(s):

Keisuke Saito ◽

Jian-Ren Shen ◽

Toyokazu Ishida ◽

Hiroshi Ishikita

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Photosystem Ii ◽

Redox Active ◽

Short Hydrogen Bond

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Asymmetry in Charge Transfer Pathways Caused by Pigment–Protein Interactions in the Photosystem II Reaction Center Complex

Catalysts ◽

10.3390/catal10060718 ◽

2020 ◽

Vol 10 (6) ◽

pp. 718

Author(s):

Yoshihiro Sato ◽

Danielle Sicotte

Keyword(s):

Charge Transfer ◽

Photosystem Ii ◽

Reaction Center ◽

Protein Interactions ◽

Energy Levels ◽

Tight Binding ◽

Relative Displacement ◽

Primary Charge Separation ◽

Binding Model ◽

Reaction Center Complex

This article discusses the photoinduced charge transfer (CT) kinetics within the reaction center complex of photosystem II (PSII RC). The PSII RC exhibits a structural symmetry in its arrangement of pigments forming two prominent branches, D1 and D2. Despite this symmetry, the CT has been observed to occur exclusively in the D1 branch. The mechanism to realize such functional asymmetry is yet to be understood. To approach this matter, we applied the theoretical tight-binding model of pigment excitations and simulated CT dynamics based upon the framework of an open quantum system. This simulation used a recently developed method of computation based on the quasi-adiabatic propagator path integral. A quantum CT state is found to be dynamically active when its site energy is resonant with the exciton energies of the PSII RC, regardless of the excitonic landscape we utilized. Through our investigation, it was found that the relative displacement between the local molecular energy levels of pigments can play a crucial role in realizing this resonance and therefore greatly affects the CT asymmetry in the PSII RC. Using this mechanism phenomenologically, we demonstrate that a near 100-to-1 ratio of reduction between the pheophytins in the D1 and D2 branches can be realized at both 77 K and 300 K. Our results indicate that the chlorophyll Chl D 1 is the most active precursor of the primary charge separation in the D1 branch and that the reduction of the pheophytins can occur within pico-seconds. Additionally, a broad resonance of the active CT state implies that a large static disorder observed in the CT state originates in the fluctuations of the relative displacements between the local molecular energy levels of the pigments in the PSII RC.

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