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 Å 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.
Komori
Hirofumi
H
Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan.
Seo
Daisuke
D
Sakurai
Takeshi
T
Higuchi
Yoshiki
Y
D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000201:enzymology*; D018360:Crystallography, X-Ray; D005287:Ferredoxin-NADP Reductase / Q000737:chemistry* / Q000378:metabolism*; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D005287:Ferredoxin-NADP Reductase