Crystal structure analysis of Bacillus subtilis ferredoxin-NADP+ oxidoreductase and the structural basis for its substrate selectivity

Bacillus subtilis yumC encodes a novel type of ferredoxin-NADP(+) oxidoreductase (FNR) with a primary sequence and oligomeric conformation distinct from those of previously known FNRs In this study, the crystal structure of B subtilis FNR (BsFNR) complexed with NADP(+) has been determined BsFNR features two distinct binding domains for FAD and NADPH in accordance with its structural similarity to Escherichia coli NADPH-thioredoxin reductase (TdR) and TdR-like protein from Thermus thermophilus HB8 (PDB code 2ZBW) The deduced mode of NADP(+) binding to the BsFNR molecule is nonproductive in that the nicotinamide and isoalloxazine rings are over 15 A apart A unique C-terminal extension, not found in E coli TdR but in TdR-like protein from T thermophilus HB8, covers the re-face of the isoalloxazine moiety of FAD In particular, Tyr50 in the FAD-binding region and His324 in the C-terminal extension stack on the si- and re-faces of the isoalloxazine ring of FAD, respectively Aromatic residues corresponding to Tyr50 and His324 are also found in the plastid-type FNR superfamily of enzymes, and the residue corresponding to His324 has been reported to be responsible for nucleotide specificity In contrast to the plastid-type FNRs, replacement of His324 with Phe or Ser had little effect on the specificity or reactivity of BsFNR with NAD(P)H, whereas replacement of Arg190, which interacts with the 2'-phosphate of NADP(+), drastically decreased its affinity toward NADPH This implies that BsFNR adopts the same nucleotide binding mode as the TdR enzyme family and that aromatic residue on the re-face of FAD is hardly relevant to the nucleotide selectivity