Recent Advances in the Structure Analysis of Rhodopseudomonas viridis Reaction Center Mutants

Sinning, Irmgard; Koepke, Jürgen; Michel, Hartmut

doi:10.1007/978-3-642-61297-8_20

Cited by 16 publications

(9 citation statements)

References 21 publications

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“…viridis re vealed that one of the m utants, referred to as T 4 (Tyr L222 to Phe) was sensitive to the urea type inhibitors [32] in common with the PS II reaction centre. In addition, the semiquinone-iron EPR sig nal of Q B-in T 4 resembled that reported for PS II [33], X-ray crystallographic analysis of the reac tion centre from T 4 with bound D C M U [34] pro vide us with potential ligand-residue binding in teractions with the D 1 protein. In light of these observations, we propose that one binding orien- tation for D C M U in the Q B-binding pocket is sta bilized by a predom inantly electrostatic interac tion between the carbonyl group (CARB) o f the herbicide and the imidazoyl side chain of His 215 (Fig.…”

Section: Resultsmentioning

confidence: 61%

“…Re placement of Val 219 by lie in line with the m uta tion inducing D C M U resistance [25] increases the interm olecular energy between the more bulky lie side chain and the DM A group (Table II) and makes binding unfavourable. Non-bonded stabili zation also occurs between the phenyl moiety (PHE) of the D C M U and Ala 251 and Asn 266 but ring stacking between this group and the side chain of Phe 255 in a similar m anner to the inter action with Phe L 216 of the bacterial reaction centre [34] was not apparent. However, replace ment o f Phe 255 by Tyr does not significantly alter the overall binding energy between DCM U and the protein (Tables II and III) in agreement with its reported failure to induce resistance to the her bicide [36], In our model, replacement of Ala 251 by Val, another m utation reported to induce resistance to DCM U [37], produces a high intermolecular ener gy between the phenylamino group (AM IN) of the herbicide and the protein as a consequence of the steric interaction with the more bulky side chain of the m utated residue (Table II).…”

Section: Resultsmentioning

confidence: 99%

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Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II

Mackay¹,

O’Malley

1993

Zeitschrift Für Naturforschung C

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Section: Resultsmentioning

confidence: 61%

Section: Resultsmentioning

confidence: 99%

Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II

Mackay¹,

O’Malley

1993

Zeitschrift Für Naturforschung C

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“…Interestingly, the binding affinity for the Rp. viridis wild-type RC of terbutryn is 14-fold higher than that of atrazine (47). The reduction in the interplanar angle between the triazine ring and Phe L216 from 24°in the case of atrazine to 17°in the case of terbutryn is probably not sufficient to explain the higher affinity by increased -interactions.…”

Section: Discussionmentioning

confidence: 91%

Structural Basis of the Drastically Increased Initial Electron Transfer Rate in the Reaction Center from a Rhodopseudomonas viridis Mutant Described at 2.00-Å Resolution

Lancaster¹,

Bibikova²,

Sabatino³

et al. 2000

Journal of Biological Chemistry

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It has previously been shown that replacement of the residue His L168 with Phe (HL168F) in the Rhodopseudomonas viridis reaction center (RC) leads to an unprecedented drastic acceleration of the initial electron transfer rate. Here we describe the determination of the x-ray crystal structure at 2.00-Å resolution of the HL168F RC. The electron density maps confirm that a hydrogen bond from the protein to the special pair is removed by this mutation. Compared with the wild-type RC, the acceptor of this hydrogen bond, the ring I acetyl group of the "special pair" bacteriochlorophyll, D L , is rotated, and its acetyl oxygen is found 1.1 Å closer to the bacteriochlorophyll-Mg Life on earth depends on the ability of photosynthetic organisms to convert solar energy into biochemically amenable energy. A central role in the photosynthetic process is played by the photosynthetic reaction center (RC), 1 an integral membrane protein-pigment complex. The RCs from purple bacteria, which catalyze the light-induced reduction of ubiquinone to ubihydroquinone (or ubiquinol) involving the uptake of two protons from the cytoplasm and the oxidation of cytochrome c 2 in the periplasm, are the best characterized membrane protein complexes (see Refs. 1-4 for reviews). The RC of the non-sulfur purple bacterium Rhodopseudomonas (Rp., more recently suggested to be reclassified as Blastochloris (5)) viridis is composed of four polypeptides, namely the L, M, H, and C (a tightly bound tetra-heme cytochrome c) subunits (6) and fourteen cofactors (four heme molecules, four bacteriochlorophyll b, two bacteriopheophytin b, one carotenoid, one non-heme iron, and two quinones, as described previously (7). The four heme molecules are covalently bound by the C subunit, and all other cofactors are non-covalently bound by the L and M subunits. The complex has eleven membrane-spanning helices, five in the L, five in the M, and one in the H subunit. Large parts of the L and M subunits and their associated cofactors are related by a 2-fold rotational symmetry axis perpendicular to the plane of the membrane (7-10). Light is absorbed by the bacteriochlorophyll of the B1015 light-harvesting antennae. Excitation energy is then transferred to a dimer of bacteriochlorophyll, the special pair D, thus forming the excited state D*. This decays to D ϩ through electron transfer via the monomeric accessory bacteriochlorophyll B A and the bacteriopheophytin A (11, 12) to the primary quinone Q A , which is a menaquinone-9 in the Rp. viridis RC. The electron is then transferred to a secondary quinone, Q B , which is ubiquinone-9 in the Rp. viridis RC. Whereas Q A can accept only one electron, Q B functions as a "two-electron gate" (13), and after a second reduction and the uptake of two protons from the cytoplasm, the ubiquinol leaves its binding site (14, 15) to be reoxidized by the cytochrome bc 1 complex (16), which results in the release of protons on the periplasmic side of the membrane. This proton transport produces a transmembrane electrochemical potential that...

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“…The DCMU structure was moved manually to match the DCMU-binding pattern determined in the crystal structure in a mutant Rps. viridis reaction center (T4) (Sinning et al, 1990;Sinning, 1992). All residues surrounding DCMU were fully energy minimized with ABNR.…”

Section: Methodsmentioning

confidence: 99%

“…viridis mutants showed that a mutation (L-Y222F) resulted in the reaction center being "PSII-like" by becoming receptive to urea type herbicides (e.g.. DCMU) (Sinning et al, 1989). The X-ray structure of this mutant (T4) reaction center with bound DCMU is available (Sinning et al, 1990;Sinning, 1992). The structure shows that the mutation eliminates the hydrogen bonding between the L-Y222 and M-D43, causing a slight movement of a stretch of M residues that shield the Q B site, thus widening the Q B binding pocket.…”

Section: Herbicide Dcmu Bindingmentioning

confidence: 99%

Modeling of the D1/D2 proteins and cofactors of the photosystem II reaction center: Implications for herbicide and bicarbonate binding

1996

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A three-dimensional model of the photosystem I1 (PSII) reaction center from the cyanobacterium Synechocystis sp. PCC 6803 was generated based on homology with the anoxygenic purple bacterial photosynthetic reaction centers of Rhodobacter sphaeroides and Rhodopseudomonas viridis, for which the X-ray crystallographic structures are available. The model was constructed with an alignment of Dl and D2 sequences with the L and M subunits of the bacterial reaction center, respectively, and by using as a scaffold the structurally conserved regions (SCRs) from bacterial templates. The structurally variant regions were built using a novel sequence-specific approach of searching for the best-matched protein segments in the Protein Data Bank with the "basic local alignment search tool" (Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, 1990, J Mol Biol 215:403-410). and imposing the matching conformational preference on the corresponding D l and D2 regions. The structure thus obtained was refined by energy minimization. The modeled D l and D2 proteins contain five transmembrane a-helices each, with cofactors (4 chlorophylls, 2 pheophytins, 2 plastoquinones, and a non-heme iron) essential for PSII primary photochemistry embedded in them. A p-carotene, considered important for PSII photoprotection, was also included in the model. Four different possible conformations of the primary electron donor P680 chlorophylls were proposed, one based on the homology with the bacterial template and the other three on existing experimental suggestions in literature. The P680 conformation based on homology was preferred because it has the lowest energy.Redox active tyrosine residues important for P680' reduction as well as residues important for PSI1 cofactor binding were analyzed. Residues involved in interprotein interactions in the model were also identified. Herbicide 3-(3,4-dichlorophenyI)-I , 1 -dimethylurea (DCMU) was also modeled in the plastoquinone QB binding niche using the structural information available from a DCMU-binding bacterial reaction center.A bicarbonate anion, known to play a role in PSII, but not in anoxygenic photosynthetic bacteria, was modeled in the non-heme iron site, providing a bidentate ligand to the iron. By modifying the previous hypothesis of Blubaugh and Govindjee (1988, Photosyn Res 1 9 3 -1 2 8 ) , we modeled a second bicarbonate and a water molecule in the Qe site and we proposed a hypothesis to explain the mechanism of QB protonation mediated by bicarbonate and water. The bicarbonate, stabilized by DLR257, donates a proton to Qi-through the intermediate of DLH252; and a water molecule donates another proton to Qi-. Based on the discovery of a "water transport channel" in the bacterial reaction center, an analogous channel for transporting water and bicarbonate is proposed in our PSII model. The putative channel appears to be primarily positively charged near QB and the non-heme iron, in contrast to the polarity distribution in the bacterial water transport channel. The constructed model has ...

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Recent Advances in the Structure Analysis of Rhodopseudomonas viridis Reaction Center Mutants

Cited by 16 publications

References 21 publications

Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II

Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II

Structural Basis of the Drastically Increased Initial Electron Transfer Rate in the Reaction Center from a Rhodopseudomonas viridis Mutant Described at 2.00-Å Resolution

Modeling of the D1/D2 proteins and cofactors of the photosystem II reaction center: Implications for herbicide and bicarbonate binding

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Recent Advances in the Structure Analysis of Rhodopseudomonas viridis Reaction Center Mutants

Cited by 16 publications

References 21 publications

Molecular Modelling of the Interaction between DCMU and the QB-Binding Site of Photosystem II

Molecular Modelling of the Interaction between DCMU and the QB-Binding Site of Photosystem II

Structural Basis of the Drastically Increased Initial Electron Transfer Rate in the Reaction Center from a Rhodopseudomonas viridis Mutant Described at 2.00-Å Resolution

Modeling of the D1/D2 proteins and cofactors of the photosystem II reaction center: Implications for herbicide and bicarbonate binding

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Product

Resources

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Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II

Molecular Modelling of the Interaction between DCMU and the Q_B-Binding Site of Photosystem II