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      An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

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          Abstract

          Photosynthetic water oxidation is catalyzed by the Mn 4CaO 5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S 0 to S 4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S 1, S 2, and S 3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S 2, but flipping of D1 Glu 189 upon transition to S 3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn 4CaO 6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

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          Linking crystallographic model and data quality.

          P. Andrew Karplus, Kay Diederichs (2012)
          In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.
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            The integration of macromolecular diffraction data.

            Andrew Leslie (2006)
            The objective of any modern data-processing program is to produce from a set of diffraction images a set of indices (hkls) with their associated intensities (and estimates of their uncertainties), together with an accurate estimate of the crystal unit-cell parameters. This procedure should not only be reliable, but should involve an absolute minimum of user intervention. The process can be conveniently divided into three stages. The first (autoindexing) determines the unit-cell parameters and the orientation of the crystal. The unit-cell parameters may indicate the likely Laue group of the crystal. The second step is to refine the initial estimate of the unit-cell parameters and also the crystal mosaicity using a procedure known as post-refinement. The third step is to integrate the images, which consists of predicting the positions of the Bragg reflections on each image and obtaining an estimate of the intensity of each reflection and its uncertainty. This is carried out while simultaneously refining various detector and crystal parameters. Basic features of the algorithms employed for each of these three separate steps are described, principally with reference to the program MOSFLM.
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              Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses.

              Michihiro Suga, Fusamichi Akita, Kunio Hirata … (2015)
              Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.
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                Author and article information

                Journal
                Title: Science
                Abbreviated Title: Science
                Publisher: American Association for the Advancement of Science (AAAS)
                ISSN (Print): 0036-8075
                ISSN (Electronic): 1095-9203
                Publication date Created: October 17 2019
                Publication date Created: October 18 2019
                Publication date (Print): October 18 2019
                Publication date (Electronic): October 17 2019
                Volume: 366
                Issue: 6463
                Pages: 334-338
                Article
                DOI: 10.1126/science.aax6998
                PubMed ID: 31624207
                SO-VID: 6557192a-199c-4862-bb41-4083f263d176
                Copyright © © 2019
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                http://www.sciencemag.org/about/science-licenses-journal-article-reuse

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