1BU5

X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex.

Walsh, M.A.McCarthy, A.O'Farrell, P.A.McArdle, P.Cunningham, P.D.Mayhew, S.G.Higgins, T.M.

(1998) Eur.J.Biochem. 258: 362-371


  • PubMed Abstract: 
  • The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex with riboflavin. The ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of FMN for flavin binding. The redox ...

    The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex with riboflavin. The ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of FMN for flavin binding. The redox potential of the semiquinone/hydroquinone couple of the bound riboflavin is 180 mV less negative than the corresponding complex with FMN. To elucidate the binding of riboflavin, the complex has been crystallized and the crystal structure solved by molecular replacement using native flavodoxin as a search model to a resolution of 0.183 nm. Compared to the FMN complex, the hydrogen-bonding network at the isoalloxazine sub-site of the riboflavin complex is severely disrupted by movement of the loop residues Ser58-Ile64 (60-loop) which contact the isoalloxazine by over 0.35 nm, and by a small displacement of the isoalloxazine moiety. The 60-loop movement away from the flavin increases the solvent exposure of the flavin-binding site. The conformation of the site at which 5'-phosphate of FMN normally binds is similar in the two complexes, but in the riboflavin complex a sulphate or phosphate ion from the crystallization buffer occupies the space. This causes small structural perturbations in the phosphate-binding site. The flexibility of the 60-loop in D. vulgaris flavodoxin appears to be a contributing factor to the binding of riboflavin by the apoprotein, and a feature that distinguishes the protein from other 'short chain' flavodoxins. In the absence of the terminal phosphate group, free movement at the 5'-OH group of the ribityl chain can occur. Thus, the 5'-phosphate of FMN secures the cofactor at the binding site and positions it optimally. The structural changes which occur in the 60-loop in the riboflavin complex probably account for most of the positive shift that is observed in the midpoint potential of the semiquinone/hydroquinone couple of the riboflavin complex compared to that of the FMN complex.


    Related Citations: 
    • The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0- Angstroms Resolution
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.
      (1973) Proc.Natl.Acad.Sci.USA 70: 3857
    • Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenictemperatures
      Watt, W.,Tulinsky, A.,Swenson, R.P.,Watenpaugh, K.D.
      (1991) J.Mol.Biol. 218: 195
    • Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough)
      Krey, G.D.,Vanin, E.F.,Swenson, R.P.
      (1988) J.Biol.Chem. 218: 15436
    • Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.,Legall, J.,Dubourdieu, M.
      (1972) Proc.Natl.Acad.Sci.USA 69: 3185
    • Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough
      Curley, G.P.,Voordouw, G.
      (1988) Fems Microbiol.Lett. 49: 295


    Organizational Affiliation

    Department of Chemistry, University College, Galway, Ireland. walsh@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FLAVODOXIN)
A, B
147Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)N/A
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P00323
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download SDF File 
Download CCD File 
A, B
RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.380α = 90.00
b = 62.310β = 127.26
c = 77.420γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CCP4refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance