3LZW

Crystal structure of ferredoxin-NADP+ oxidoreductase from bacillus subtilis (form I)

Summary for 3LZW

• Entry DOI: 10.2210/pdb3lzw/pdb
• Related: 3LZX
• Descriptor: Ferredoxin--NADP reductase 2, FLAVIN-ADENINE DINUCLEOTIDE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (5 entities in total)
• Functional Keywords: ferredoxin reductase, fad, nadph, flavoprotein, nadp, oxidoreductase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 38459.89

Authors

Komori, H.,Seo, D.,Sakurai, T.,Higuchi, Y. (deposition date: 2010-03-02, release date: 2010-12-08, Last modification date: 2023-11-01)

Primary citation

Komori, H.,Seo, D.,Sakurai, T.,Higuchi, Y.
Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity
Protein Sci., 19:2279-2290, 2010

PubMed Abstract: 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.

PubMed: 20878669
DOI: 10.1002/pro.508

Experimental method

X-RAY DIFFRACTION (1.8 Å)