Abstract
Flavodoxins, which exist widely in microorganisms, have been found in various pathways with multiple physiological functions. The flavodoxin (Fld) containing the cofactor flavin mononucleotide (FMN) from sulfur-reducing bacteria Desulfovibrio gigas (D. gigas) is a short-chain enzyme that comprises 146 residues with a molecular mass of 15 kDa and plays important roles in the electron-transfer chain. To investigate its structure, we purified this Fld directly from anaerobically grown D. gigas cells. The crystal structure of Fld, determined at resolution 1.3 Å, is a dimer with two FMN packing in an orientation head to head at a distance of 17 Å, which generates a long and connected negatively charged region. Two loops, Thr59–Asp63 and Asp95–Tyr100, are located in the negatively charged region and between two FMN, and are structurally dynamic. An analysis of each monomer shows that the structure of Fld is in a semiquinone state; the positions of FMN and the surrounding residues in the active site deviate. The crystal structure of Fld from D. gigas agrees with a dimeric form in the solution state. The dimerization area, dynamic characteristics and structure variations between monomers enable us to identify a possible binding area for its functional partners.
Highlights
The electron-transfer chains are the critical reactions, such as the photosynthesis and respiration systems, for the production of biological energy
Superimposed structures of two monomers from the D. gigas Fld dimer reveal that those corresponding residues are deviated with different orientations, implying that a similar modulation of the redox potential might exist in D. gigas Fld
The crystal structure of Fld from D. gigas might explain that the dimeric form is the functional unit due to the aligned negatively charged region formed by dimerization, in which two flexible loops might serve for the protein-partner recognition
Summary
The electron-transfer chains are the critical reactions, such as the photosynthesis and respiration systems, for the production of biological energy. Some studies showed that cytochrome c3 and Fld might form a protein complex [26], the exact pathway of the electron transfer between the periplasm and the sulfate-reducing system remains unclear. The effects of some mutated residues, such as G61V and D95E, interacting with the FMN in three redox states were studied in D. vulgaris Fld [29,30]. Based on their molecular mass, the Flds are classifiable into two groups: the “long-chain” Flds containing about 169–176 amino acids and the “short-chain” enzymes lacking ~20–30 residues at the middle region of the sequences in comparison between these two groups, of which the physiological function is unknown. 1.3 Å; we study its structural-functional relationship and the prospective binding region for an electron-transferring partner
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