1FDD

AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Azotobacter vinelandii ferredoxin I. Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster.

Shen, B.Martin, L.L.Butt, J.N.Armstrong, F.A.Stout, C.D.Jensen, G.M.Stephens, P.J.La Mar, G.N.Gorst, C.M.Burgess, B.K.

(1993) J.Biol.Chem. 268: 25928-25939


  • PubMed Abstract: 
  • The [3Fe-4S]+/0 cluster of Azotobacter vinelandii ferredoxin I (AvFdI) has an unusually low and strongly pH-dependent reduction potential (E'0). The reduced cluster exists in two forms, depending upon pH, that exhibit substantially different magnetic ...

    The [3Fe-4S]+/0 cluster of Azotobacter vinelandii ferredoxin I (AvFdI) has an unusually low and strongly pH-dependent reduction potential (E'0). The reduced cluster exists in two forms, depending upon pH, that exhibit substantially different magnetic circular dichroism (MCD) spectra. Recent studies have established that the MCD changes observed on decreasing the pH from 8.3 (alkaline form) to 6.0 (acid form) cannot be explained either by a change in spin state of the cluster (Stephens, P.J., Jensen, G.M., Devlin, F.J., Morgan, T.V., Stout, C. D., Martin, A.E., and Burgess, B.K. (1991) Biochemistry 30, 3200-3209) or by a major structural change (e.g. ligand exchange) (Stout, C.D. (1993) J. Biol. Chem. 268, 25920-25927). Here, we have examined the influence of aspartate 15 on the pH dependence of the spectroscopic and electrochemical properties of AvFdI by construction of a D15N mutant. Aspartate 15, which is salt-bridged to lysine 84 at the protein surface, is the closest ionizable residue to the [3Fe-4S] cluster. The results show that replacement of aspartate by asparagine results in an approximately 20-mV increase in E'0 for the [3Fe-4S]+/0 cluster at high pH concomitant with an approximately 0.8-pH unit decrease in the pK of the reduced form. The major pH dependence of E'0 is preserved as is the effect observed by MCD. These data eliminate the possibility that the MCD change is due to the presence of Asp-15 and support the conclusion that it originates in direct protonation of the [3Fe-4S]0 cluster, probably on a sulfide ion. Voltammetric studies show that interconversion between [3Fe-4S]+ and [3Fe-4S]0 at acidic pH involves rapid electron transfer followed by proton transfer (for reduction) and then proton transfer followed by electron transfer (for oxidation). Ionized aspartate 15 facilitates proton transfer. Thus, protonation and deprotonation are much slower for D15N relative to the native protein at pH > 5.5. Proton transfer reactions necessary for further reduction of the [3Fe-4S]0 cluster to the [3Fe-4S]- and [3Fe-4S]2- states are also retarded in D15N. The results suggest that the carboxylate-ammonium salt bridge afforded by Asp-15-Lys-84 conducts protons between the cluster and solvent H2O molecules. Overproduction of D15N FdI, but not native FdI, in A. vinelandii has a negative effect on the growth rate of the organism, suggesting that the rate of protonation or deprotonation of the [3Fe-4S]0 cluster may be important in vivo.


    Related Citations: 
    • Two Crystal Forms of Azotobacter Ferredoxin
      Stout, C.D.
      (1979) J.Biol.Chem. 254: 3598
    • 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
    • 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
    • Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin
      Soman, J.,Iismaa, S.,Stout, C.D.
      (1991) J.Biol.Chem. 266: 21558
    • 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
    • 7-Iron Ferredoxin Revisited
      Stout, C.D.
      (1988) J.Biol.Chem. 263: 9256
    • Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution
      Stout, C.D.
      (1989) J.Mol.Biol. 205: 545
    • 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
    • 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
    • Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii
      Ghosh, D.,Fureyjunior, W.,O'Donnell, S.,Stout, C.D.
      (1981) J.Biol.Chem. 256: 4185
    • (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


    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 vinelandiiGene 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: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.600α = 90.00
b = 55.600β = 90.00
c = 95.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-01-17 
  • Released Date: 1993-10-31 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance