X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex

The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex wi th riboflavin. The ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of FMN for flavin binding. The redox potential of the semiquinone/hydroquinone couple of the bound riboflavin is 180 mV less negative than the corresponding comp lex with FICIN, To elucidate the binding of riboflavin, the complex has bee n crystallized and the crystal structure solved by molecular replacement us ing native flavodoxin as a search model to a resolution of 0.183 nm. Compar ed to the FMN complex, the hydrogen-bonding network at the isoalloxazine su b-site of the riboflavin complex is severely disrupted by movement of the l oop residues Ser58 - Ile64 (60-loop) which contact the isoalloxazine by ove r 0.35 nm, and by a small displacement of the isoalloxazine moiety. The 60- loop movement away from the flavin increases the solvent exposure of the fl avin-binding site. The conformation of the site at which 5'-phosphate of FM N normally binds is similar in the two complexes, but in the riboflavin com plex a sulphate or phosphate ion from the crystallization buffer occupies t he space. This causes small structural perturbations in the phosphate-bindi ng site. The flexibility of the 60-loop in D, vulgar is flavodoxin appears to be a contributing factor to the binding of riboflavin by the apoprotein, and a feature that distinguishes the protein from other 'short chain' flav odoxins. In the absence of the terminal phosphate group, free movement at t he 5'-OH group of the ribityl chain can occur. Thus, the 5'-phosphate of FM N secures the cofactor at the binding site and positions it optimally. The structural changes which occur in the 60-loop in the riboflavin complex pro bably account for most of the positive shift that is observed in the midpoi nt potential of the semiquinone/hydroquinone couple of the riboflavin compl ex compared to that of the FMN complex.