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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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

Komori, H.Seo, D.Sakurai, T.Higuchi, Y.

(2010) Protein Sci 19: 2279-2290

  • DOI: https://doi.org/10.1002/pro.508
  • Primary Citation of Related Structures:  
    3LZW, 3LZX

  • 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.

  • Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--NADP reductase 2332Bacillus subtilisMutation(s): 0 
Find proteins for O05268 (Bacillus subtilis (strain 168))
Explore O05268 
Go to UniProtKB:  O05268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05268
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NAP Binding MOAD:  3LZW Kd: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.9α = 90
b = 135.724β = 90
c = 39.191γ = 90
Software Package:
Software NamePurpose
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description