3A20

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1093/jb/mvm051
  • Primary Citation of Related Structures:  
    3A20, 1WLK, 1WLI

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FMN-binding proteinAB122Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 1 
Gene Names: DvMF_2023
Find proteins for Q46604 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore Q46604 
Go to UniProtKB:  Q46604
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd:  1.1200000047683716   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-04-27 
  • Released Date: 2009-05-19 
  • Deposition Author(s): Shibata, N., Higuchi, Y.
  • This entry supersedes: 1WLL

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance