An x-ray absorption study of the iron site in bacterial photosynthetic reaction centers

Bunker, Grant; Stern, Edward A.; Blankenship, Robert E.; Parson, Walther

doi:10.1016/s0006-3495(82)84699-7

Cited by 68 publications

(42 citation statements)

References 25 publications

(33 reference statements)

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“…That the iron is approximately equidistant from both quinones was suggested from an analysis of EPR data (28). The structure near the iron is in good agreement with the conclusions drawn from extended x-ray adsorption (EXAFS) studies (29,30). A striking feature of the RC is the presence of the membrane-spanning helices.…”

Section: Resultssupporting

confidence: 76%

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Allen¹,

Fehér²,

Yeates³

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

347

165

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Crystals of the reaction center (RC) from RCs from purple photosynthetic bacteria contain three subunits, L, M, and H (present in a 1:1:1 stoichiometry) and a number of cofactors: four bacteriochlorophylls (BChls), two bacteriopheophytins, two quinones, QA (primary electron acceptor), and QB (secondary electron acceptor), and one nonheme iron (for reviews, see refs. 1 and 2). Although RCs from different species exhibit many similarities in structure, there are some significant structural differences.The RCs from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis that are the subject of this investigation show the following differences. In R. sphaeroides the secondary, water-soluble cytochrome is not present in purified RCs. In contrast, RCs from R. viridis contain a fourth subunit, a cytochrome, that has four heme groups associated with it. The two species contain different types of BChl: R. sphaeroides has BChl-a whereas R. viridis contains BChl-b. The primary quinone in R. sphaeroides is a ubiquinone, whereas in R. viridis it is a menaquinone. Furthermore, the two quinones that serve as acceptors are retained in purified RCs from R. sphaeroides, but one is apparently lost from R. viridis during the purification.Although extensive work has been done during the past two decades to characterize RCs, until recently there was very little information available on their three-dimensional structure. The reason was the lack of crystals suitable for x-ray diffraction studies. This situation changed with the successful crystallization of RCs from R. viridis (3) and R. sphaeroides (4, §). These crystals are of sufficient size and quality to obtain good x-ray diffraction data. The structure of the RCs from R. viridis has been reported recently at a resolution of 3 A (5, 6).In this work we describe the use of the Patterson search (molecular replacement) method (for reviews, see refs. 7 and 8) to obtain a low-resolution electron density map of the RC from R. sphaeroides and to show the homology between the structures of the RCs from the two bacterial species. A preliminary account of this work has been presented (9).EXPERIMENTAL PROCEDURES Crystallization. The RC from R. sphaeroides was crystallized by using the vapor diffusion technique. Different crystallization conditions produced a variety of forms as reported (4,10,11). The crystal form used for these structural studies was grown under the following conditions. The initial protein solution consisted of 5 mg of RC per ml, 0.36 M NaCl, 3.9%

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Section: Resultssupporting

confidence: 76%

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Allen¹,

Fehér²,

Yeates³

et al. 1986

Proc. Natl. Acad. Sci. U.S.A.

347

165

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“…Helices IV and V of each subunit are of particular relevance of quinone and herbicide binding. As already proposed from EXAF studies (34) and now seen in the X-ray structure (32,33) of the bacterial system, histidines are responsible for Fe binding. Four histidines are involved according to the X-ray structure and these are conserved in the D-I/D-2 subunits: his 215 and his 272 in the D-I and the homologous his 215 and his 269 in the D-2 polypeptide.…”

Section: [236]mentioning

confidence: 64%

Inhibitors of photosystem II and the topology of the herbicide and QB binding polypeptide in the thylakoid membrane

1986

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The folding through the thylakoid membrane of the D-1 herbicide binding polypeptide and of the homologous D-2 subunit of photosystem II is predicted from comparison of amino acid sequences and hydropathy index plots with the folding of the subunits L and M of a bacterial photosystem. As the functional amino acids involved in Q and Fe binding in the bacterial photosystem of R. viridis, as indicated by the X-ray structure, are conserved in the homologous D-1 and D-2 subunits of photosystem II, a detailed topology of the binding niche of QB and of herbicides on photosystem II is proposed. The model is supported by the observed amino acid changes in herbicide tolerant plants and algae. These changes are all in the binding domain on the matrix side of the D-1 polypeptide, and turn out to be of functional significance in the QB binding.New inhibitors of QB function are described. Their chemical structure, i.e. pyridones, quinolones, chromones and benzodiones, contains the features of the phenolic type herbicides. Their essential elements, π-charges at particular atoms, QSAR and steric requirements for optimal inhibitory potency are discussed and compared with the "classical" herbicides of the urea/triazine type.

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“…These include magnetic susceptibility measurements (45), Mossbauer spectroscopy (46), extended x-ray fine structure absorption (47,48), and EPR (49,50). The conclusions about the Fe2+ arrived at from these experiments are (i) it is in a high spin Fe2+ state irrespective of the oxidation state of the quinone acceptors (45,46); (ii) it does not form a direct ligand to the quinones (45)(46)(47)(48)(49); (iii) it interacts magnetically with the unpaired electron on the quinone (45,49,50); (iv) its most likely number of ligands is six, with an average bond length of 2.12 ± 0.03 A (47,48); (v) its environment is a distorted octahedron (45)(46)(47)(48)(49); (vi) it is closer to QB than to QA (49). It was originally thought that the Fe2+ may play an important role in the electron transfer from QA and QB (6,51).…”

Section: Resultsmentioning

confidence: 99%

Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors.

Allen

Fehér²,

Yeates³

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

903

608

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The three-dimensional structure of the cofactors of the reaction center of Rhodobacter sphaeroides R-26 has been determined by x-ray diffraction and refined at a resolution of 2.8 A with an R value of 26%. The main features of the structure are similar to the ones determined for Rhodopseudomonas viridis [Michel, H., Epp, 0. & Deisenhofer, J. (1986) EMBO J. 5, 2445EMBO J. 5, -2451. The cofactors are arranged along two branches, which are approximately related to each other by a 2-fold symmetry axis. The structure is well suited to produce light-induced charge separation across the membrane. Most of the structural features predicted from physical and biochemical measurements are confirmed by the x-ray structure.The reaction center (RC) is an integral membrane proteinpigment complex that mediates the primary processes of photosynthesis-i.e., the light-induced electron transfers from a donor to a series of acceptor species. The three-dimensional structure of the RC from the photosynthetic bacterium Rhodopseudomonas viridis has recently been determined by x-ray diffraction at a resolution of 2.9 A (1-3). In this paper, we report the structure analysis of the RC from another purple bacterium, the carotenoidless mutant R-26 of Rhodobacter sphaeroides (previously called Rhodopseudomonas sphaeroides). The motivation for undertaking the structure determination of the RC of a second bacterial species was 2-fold. (i) The RC from Rb. sphaeroides has been investigated for the past two decades and, consequently, is the best characterized RC (for reviews see refs. 4 and 5); in addition, the methodologies for manipulating its structure (e.g., exchanging cofactors, dissociating and reassociating the subunits) have been worked out in detail (4-10). (ii) The availability of structures from two organisms may help in elucidating structure-function relationships by correlating differences in structure with differences in function.The RC from Rb. sphaeroides is composed of three protein subunits-L, M, and H-and the following cofactors: four bacteriochlorophylls (Bchls), two bacteriopheophytins (Bphes), two ubiquinones, and one nonheme iron. The RC from R. viridis has an additional subunit, a cytochrome with four c-type hemes; its Bchls and Bphes are of the "b" type instead of the "a" type found in Rb. sphaeroides, and its primary quinone is a menaquinone. Notwithstanding these differences, the two structures were found to be very similar. This made it possible to use the method of molecular replacement (11) to solve the phase problem in the x-ray analysis (12)(13)(14). The crystals of Rb. sphaeroides diffract at least to a resolution of 2.6 A and retain the ability to perform the primary photochemistry (15). We have solved the structure of the protein and the cofactors to a resolution of 2.8 A with an R factor of 26%. In this paper, we report the structure of the cofactors. The structure of the protein, the relation of the RC protein to the membrane, and the interaction of the cofactors with the protein will be reported in ...

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An x-ray absorption study of the iron site in bacterial photosynthetic reaction centers

Cited by 68 publications

References 25 publications

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Structural homology of reaction centers from Rhodopseudomonas sphaeroides and Rhodopseudomonas viridis as determined by x-ray diffraction.

Inhibitors of photosystem II and the topology of the herbicide and QB binding polypeptide in the thylakoid membrane

Structure of the reaction center from Rhodobacter sphaeroides R-26: the cofactors.

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