Rationalizing the 1.9 Å Crystal Structure of Photosystem II-A Remarkable Jahn-Teller Balancing Act Induced by a Single Proton Transfer

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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WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633613410022 ◽

2013 ◽

Vol 12 (08) ◽

pp. 1341002 ◽

Cited By ~ 1

Author(s):

XIN ZHANG ◽

MING LEI

Keyword(s):

Crystal Structure ◽

Molecular Dynamics ◽

Hydrogen Bonds ◽

Proton Transfer ◽

Glutamic Acid ◽

Active Site ◽

Nucleophilic Attack ◽

Zinc Ions ◽

Initial Model ◽

Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

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The crystal structure of szenicsite, Cu3MoO4(OH)4

Mineralogical Magazine ◽

10.1180/002646198547837 ◽

1998 ◽

Vol 62 (04) ◽

pp. 461-469 ◽

Cited By ~ 7

Author(s):

Peter C. Burns

Keyword(s):

Crystal Structure ◽

Goodness Of Fit ◽

Direct Methods ◽

Ligand Field ◽

Area Detector ◽

Vertex Sharing ◽

Distorted Octahedral ◽

Jahn Teller ◽

Jahn Teller Effect ◽

Least Squares Techniques

Abstract The crystal structure of szenicsite, Cu3MoO4(OH)4, orthorhombic, a = 8.5201(8), b = 12.545(1), c = 6.0794(6) Å, V = 649.8(2) Å3, space group Pnnm, Z = 4, has been solved by direct methods and refined by least-squares techniques to an agreement index (R) of 3.34% and a goodness-of-fit (S) of 1.11 for 686 unique observed [|F| ⩾ 4σF] reflections collected using graphite-monochromated Mo-Kα X-radiation and a CCD area detector. The structure contains three unique Cu2+ positions that are each coordinated by six anions in distorted octahedral arrangements; the distortions of the octahedra are due to the Jahn-Teller effect associated with a d 9 metal in an octahedral ligand-field. The single unique Mo6+ position is tetrahedrally coordinated by four O2− anions. The Cu2+ϕ6 (ϕ: unspecified ligand) octahedra share trans edges to form rutile-like chains, three of which join by the sharing of octahedral edges to form triple chains that are parallel to [001]. The MoO4 tetrahedra are linked to either side of the triple chain of Cu2+ϕ6 octahedra by the sharing of two vertices per tetrahedron, and the resulting chains are cross-linked through tetrahedral-octahedral vertex sharing to form a framework structure. The structure of szenicsite is closely related to that of antlerite, Cu3SO4(OH)4, which contains similar triple chains of edge-sharing Cu2+ϕ6 octahedra.

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Observation of a single proton transfer fluorescence in a biaxially symmetric dihydroxy diflavonol

Chemical Physics Letters ◽

10.1016/s0009-2614(01)01490-7 ◽

2002 ◽

Vol 352 (5-6) ◽

pp. 415-420 ◽

Cited By ~ 13

Author(s):

Elena Falkovskaia ◽

Vasyl G. Pivovarenko ◽

Juan Carlos del Valle

Keyword(s):

Proton Transfer ◽

Single Proton

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Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism

Biochemical Journal ◽

10.1042/bj3590065 ◽

2001 ◽

Vol 359 (1) ◽

pp. 65-75 ◽

Cited By ~ 25

Author(s):

Valeria MENCHISE ◽

Catherine CORBIER ◽

Claude DIDIERJEAN ◽

Michele SAVIANO ◽

Ettore BENEDETTI ◽

...

Keyword(s):

Crystal Structure ◽

Proton Transfer ◽

Chlamydomonas Reinhardtii ◽

Catalytic Mechanism ◽

Structural Data ◽

Careful Analysis ◽

Wild Type ◽

Thioredoxin H ◽

Dynamics Simulations

Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.

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