1FD2

SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I. (FE-S) CLUSTER-DRIVEN PROTEIN REARRANGEMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement.

Martin, A.E.Burgess, B.K.Stout, C.D.Cash, V.L.Dean, D.R.Jensen, G.M.Stephens, P.J.

(1990) Proc.Natl.Acad.Sci.USA 87: 598-602

  • DOI: 10.1073/pnas.87.2.598

  • PubMed Abstract: 
  • Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced ...

    Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here we report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure.


    Related Citations: 
    • 7-Iron Ferredoxin Revisited
      Stout, C.D.
      (1988) J.Biol.Chem. 263: 9256
    • Two Crystal Forms of Azotobacter Ferredoxin
      Stout, C.D.
      (1979) J.Biol.Chem. 254: 3598
    • Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
      Stout, C.D.
      (1979) Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) 6: 97
    • Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
      Stout, C.D.
      (1989) J.Mol.Biol. 205: 545
    • Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution
      Ghosh, D.,O'Donnell, S.,Fureyjunior, W.,Robbins, A.H.,Stout, C.D.
      (1982) J.Mol.Biol. 158: 73
    • (4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein
      Stephens, P.J.,Morgan, T.V.,Devlin, F.,Penner-Hahn, J.E.,Hodgson, K.O.,Scott, R.A.,Stout, C.D.,Burgess, B.K.
      (1985) Proc.Natl.Acad.Sci.USA 82: 5661
    • Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues
      Howard, J.B.,Lorsbach, T.W.,Ghosh, D.,Melis, K.,Stout, C.D.
      (1983) J.Biol.Chem. 258: 508
    • Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii
      Ghosh, D.,Fureyjunior, W.,O'Donnell, S.,Stout, C.D.
      (1981) J.Biol.Chem. 256: 4185
    • Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution
      Stout, C.D.,Ghosh, D.,Pattabhi, V.,Robbins, A.H.
      (1980) J.Biol.Chem. 255: 1797
    • Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution
      Stout, C.D.
      (1979) Nature 279: 83
    • Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin
      Soman, J.,Iismaa, S.,Stout, C.D.
      (1991) J.Biol.Chem. 266: 21558


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine 92717.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERREDOXIN
A
106Azotobacter vinelandiiMutation(s): 0 
Gene Names: fdxA
Find proteins for P00214 (Azotobacter vinelandii)
Go to UniProtKB:  P00214
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.232 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.000α = 90.00
b = 55.000β = 90.00
c = 95.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1988-12-08 
  • Released Date: 1989-10-15 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 1989-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance