1DE0

MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE NITROGENASE FE PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein.

Jang, S.B.Seefeldt, L.C.Peters, J.W.

(2000) Biochemistry 39: 641-648


  • PubMed Abstract: 
  • Protein-bound [FeS] clusters function widely in biological electron-transfer reactions, where their midpoint potentials control both the kinetics and thermodynamics of these reactions. The polarity of the protein environment around [FeS] clusters app ...

    Protein-bound [FeS] clusters function widely in biological electron-transfer reactions, where their midpoint potentials control both the kinetics and thermodynamics of these reactions. The polarity of the protein environment around [FeS] clusters appears to contribute largely to modulating their midpoint potentials, with local protein dipoles and water dipoles largely defining the polarity. The function of the [4Fe-4S] cluster containing Fe protein in nitrogenase catalysis is, at least in part, to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. Phenylalanine at position 135 is located near the [4Fe-4S] cluster of nitrogenase Fe protein and has been suggested by amino acid substitution studies to participate in defining both the midpoint potential and the nucleotide-induced changes in the [4Fe-4S] cluster. In the present study, the crystal structure of the Azotobacter vinelandii nitrogenase Fe protein variant having phenylalanine at position 135 substituted by tryptophan has been determined by X-ray diffraction methods and refined to 2.4 A resolution. A comparison of available Fe protein structures not only provides a structural basis for the more positive midpoint potential observed in the tryptophan substituted variant but also suggests a possible general mechanism by which the midpoint potential could be controlled by nucleotide interactions and nitrogenase complex formation.


    Related Citations: 
    • Crystallographic Structure of the Nitrogenase Iron Protein from Azotobacter vinelandii
      Georgiadis, M.M.,Komiya, H.,Chakrabarti, P.,Woo, D.,Kornuc, J.J.,Rees, D.C.
      (1992) Science 257: 1653
    • Conformational Variability in Structures of the Nitrogenase Iron Proteins from Azotobacter vinelandii and Clostridium pasteurianum
      Schlessman, J.L.,Woo, D.,Joshua-Tor, L.,Howard, J.B.,Rees, D.C.
      (1998) J.Mol.Biol. 280: 669
    • Structure of ADP x AlF4(-)-stabilized Nitrogenase Complex and its Implications for Signal Transduction
      Schindelin, H.,Kisker, C.,Schlessman, J.L.,Howard, J.B.,Rees, D.C.
      (1997) Nature 387: 370


    Organizational Affiliation

    Department of Chemistry, Utah State University, Logan, Utah 84322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROGENASE IRON PROTEIN
A, B
289Azotobacter vinelandiiGene Names: nifH1
EC: 1.18.6.1
Find proteins for P00459 (Azotobacter vinelandii)
Go to UniProtKB:  P00459
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.540α = 90.00
b = 91.050β = 99.76
c = 63.350γ = 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

Revision History 

  • Version 1.0: 2000-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description