Leptolyngbya boryana Ferredoxin

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

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A new structural insight into differential interaction of cyanobacterial and plant ferredoxins with nitrite reductase as revealed by NMR and X-ray crystallographic studies

Sakakibara, Y.Kimura, H.Iwamura, A.Saitoh, T.Ikegami, T.Kurisu, G.Hase, T.

(2012) J Biochem 151: 483-492

  • DOI: https://doi.org/10.1093/jb/mvs028
  • Primary Citation of Related Structures:  
    3B2F, 3B2G

  • PubMed Abstract: 

    Ferredoxin (Fd), which plays a pivotal role in photosynthesis as an electron carrier, forms a transient complex with various Fd-dependent enzymes, such as nitrite reductase (NiR), to achieve efficient intermolecular electron transfer. We studied the protein-protein interaction of Fd and NiR by NMR spectroscopy and determined three acidic regions of Fd to be major sites for the interaction with NiR, indicating that the complex is stabilized through electrostatic interaction. During this study, we found Fds from higher plant and cyanobacterium, in spite of their high structural similarities including the above acidic regions, differ remarkably in the interaction with cyanobacterial NiR. In activity assay of NiR, K(m) value for maize Fd (74.6 µM) was 9.6 times larger than that for Leptolyngbya boryana Fd (7.8 µM). The two Fds also showed a similar difference in binding assay to NiR-immobilized resin. Comparative site-specific mutagenesis of two Fds revealed that their discriminative ability for the interaction with NiR is attributed mainly to non-charged residues in the peripheral region of [2Fe-2S] cluster. These non-charged residues are conserved separately between Fds of plant and cyanobacterial origins. Our data highlight that intermolecular force(s) other than electrostatic attraction is(are) also crucial for the molecular interaction between Fd and partner enzyme.

  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. enzyme@protein.osaka-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
98Leptolyngbya boryanaMutation(s): 0 
Gene Names: petF1
Find proteins for Q51577 (Leptolyngbya boryana)
Explore Q51577 
Go to UniProtKB:  Q51577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51577
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.141α = 90
b = 34.158β = 107.3
c = 48.604γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Refinement description