Structure of the reaction center from Rhodobacter sphaeroides R-26: protein-cofactor (quinones and Fe2+) interactions.

Abstract

The three-dimensional structure of the reaction center (RC) from Rhodobacter sphaeroides has been determined by x-ray diffraction to a resolution of 2.8 A with an R value of 24%. The interactions of the protein with the primary quinone, QA, secondary quinone, QB and the nonheme iron are described and compared to those of RCs from Rhodopseudomonas viridis. Structural differences between the QA and QB environments that contribute to the function of the quinones (the electron transfer from QA to QB and the charge recombination of Q-, Q-with the primary donor) are delineated. The protein residues that may be involved in the protonation of QB are identified. A pathway for the doubly reduced QB to dissociate from the RC is proposed. The interactions between QB and the residues that have been changed in herbicide-resistant mutants are described. The environment of the nonheme iron is compared to the environments of metal ions in other proteins.The reaction center (RC) is a protein-pigment complex that mediates the primary photochemistry of photosynthetic systems. The RC from Rhodobacter sphaeroides R-26 is composed of three protein subunits (L, M, and H) and several cofactors (for a review, see ref. 1). Serving as electron acceptors are the primary quinone QA and the secondary quinone QB. In Rb. sphaeroides both quinones are ubiquinones, whereas in Rhodopseudomonas viridis QA is a menaquinone and QB is a ubiquinone.The three-dimensional structure of the RC from Rb. sphaeroides R-26 has been obtained to a resolution of2.8 A (2-4) and an R value of 24%. In this paper, we describe the interactions of the protein with the quinones and the nonheme iron. We emphasize structural features that appear to be important in electron and proton transfer. Differences in the interactions of the protein with the quinones in Rb. sphaeroides and Rps. viridis are described, although a detailed comparison between the QB interactions is difficult because of the low occupancy of the QB sites in crystals ofRps. viridis (5, 6). The interactions with the nonheme iron are found to be very similar for the two bacterial species. The interactions ofthe protein with the other cofactors as well as the crystallographic procedures have been reported (7). In a subsequent paper (8), the asymmetries ofthe two branches of the cofactors and a comparison of RCs from different species will be presented. RESULTSThe Primary Quinone. The primary quinone, QAI is located near the cytoplasmic side of the RC. Its position and orientation are well defined by the electron density, although there is no steric hindrance to moving the quinone to a position indicated by the dotted line in Fig. 1 (see below). The normal of the quinone ring forms an angle of =60°with respect to the membrane normal as defined by the direction of the twofold symmetry axis (4). QA interacts with the amino acid residues of the D, de, and E helices of the M subunit (3) (see Fig. 1).The two carbonyl oxygens Of QA are within hydrogenbonding distance to the peptide nitrogen of Ala M260 and ...

Interactions between lipids and bacterial reaction centers determined by protein crystallography

“…The overall structure of the protein is very similar to previous models of the RC from R. sphaeroides (5,8,(18)(19)(20), with no significant alterations of the cofactor organization or interactions between the cofactors and protein side chains. However, unlike previous models, the current model does include three bound lipids on the surface of the protein.…”

Solubility diagram of theRhodobacter sphaeroidesreaction center as a function of PEG concentration

“…Nevertheless progress in crystallization of membrane proteins was slow and the 3D structure determinations of membrane proteins are still rare [4][5][6][7][8][9][10][11][12][13]. The numerous difficulties in crystallization of membrane protein have encouraged crystallogenesis studies on this topic, especially on detergents effects.…”

Crystallization and X‐ray analysis of the reaction center from the thermophilic green bacterium Chloroflexus aurantiacus

“…Although crystallization of Cf aurantiacus RC can be achieved under various conditions in the presence of different detergents, it is still difficult to consistently obtain well-or- [2][3][4][5][6]. Consequently, the number of molecules per asymmetric unit cannot be deduced unequivocally.…”

“…viridis and Rb. sphaeroides have been crystallized and their structures elucidated at atomic resolution [2][3][4][5][6]. Most RCs are comprised of three protein subunits which are called H (heavy), M (medium) and L (light) according to their electrophoretic mobilities in SDS-PAGE.…”