L122K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

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Determination of the role of the Carboxyl-terminal leucine-122 in FMN-binding protein by mutational and structural analysis

Kitamura, M.Terakawa, K.Inoue, H.Hayashida, T.Suto, K.Morimoto, Y.Yasuoka, N.Shibata, N.Higuchi, Y.

(2007) J Biochem 141: 459-468

  • DOI: https://doi.org/10.1093/jb/mvm051
  • Primary Citation of Related Structures:  
    1WLI, 1WLK, 3A20

  • PubMed Abstract: 

    Mutants of flavin mononucleotide-binding protein (FMN-bp) were made by site-directed mutagenesis to investigate the role of carboxyl-terminal Leu122 of the pairing subunit in controlling redox potentials, binding the prosthetic group, and forming the tertiary and quaternary structure. We compared the oxidation-reduction potentials, FMN-binding properties, and higher structures of wild-type FMN-bp and four mutant proteins (L122Y, L122E, L122K and L122-deleted). We found that the redox potentials were affected by mutations. Also, the affinities of L122E, L122K and L122 deletion mutant apoproteins for FMN were lower than for the wild-type apoprotein, whereas the affinity of L122Y for FMN was increased. Analytical ultracentrifugation showed that the dissociation constants for dimerization of L122E and L122K were larger than for wild-type FMN-bp, whereas the dissociation constants for L122Y and the deletion mutant were lower than for the wild type. Finally, we determined the higher structures of L122Y, L122E and L122K mutants by X-ray crystallography. Our results show that the mutation of Leu122 in FMN-bp changes midpoint potentials, dissociation constants for FMN, and dimer formation, indicating that this residue is important in the pairing subunit.

  • Organizational Affiliation

    Department of Applied and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto, Osaka, Japan. kitamura@bioa.eng.osaka-cu.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN-binding protein
A, B
122Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 1 
Gene Names: DvMF_2023
Find proteins for Q46604 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore Q46604 
Go to UniProtKB:  Q46604
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46604
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FMN Binding MOAD:  3A20 Kd: 1.12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.724α = 90
b = 83.319β = 93.86
c = 40.408γ = 90
Software Package:
Software NamePurpose
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: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description