6RK0

Structure of the Flavocytochrome Anf3 from Azotobacter vinelandii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacteriumAzotobacter vinelandii.

Varghese, F.Kabasakal, B.V.Cotton, C.A.R.Schumacher, J.Rutherford, A.W.Fantuzzi, A.Murray, J.W.

(2019) J Biol Chem 294: 9367-9376

  • DOI: https://doi.org/10.1074/jbc.RA118.007285
  • Primary Citation of Related Structures:  
    6RK0

  • PubMed Abstract: 

    The biological route for nitrogen gas entering the biosphere is reduction to ammonia by the nitrogenase enzyme, which is inactivated by oxygen. Three types of nitrogenase exist, the least-studied of which is the iron-only nitrogenase. The Anf3 protein in the bacterium Rhodobacter capsulatus is essential for diazotrophic ( i.e. nitrogen-fixing) growth with the iron-only nitrogenase, but its enzymatic activity and function are unknown. Here, we biochemically and structurally characterize Anf3 from the model diazotrophic bacterium Azotobacter vinelandii Determining the Anf3 crystal structure to atomic resolution, we observed that it is a dimeric flavocytochrome with an unusually close interaction between the heme and the FAD cofactors. Measuring the reduction potentials by spectroelectrochemical redox titration, we observed values of -420 ± 10 and -330 ± 10 mV for the two FAD potentials and -340 ± 1 mV for the heme. We further show that Anf3 accepts electrons from spinach ferredoxin and that Anf3 consumes oxygen without generating superoxide or hydrogen peroxide. We predict that Anf3 protects the iron-only nitrogenase from oxygen inactivation by functioning as an oxidase in respiratory protection, with flavodoxin or ferredoxin as the physiological electron donors.


  • Organizational Affiliation

    From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom j.w.murray@imperial.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
225Azotobacter vinelandii DJMutation(s): 0 
Gene Names: Avin_49040
UniProt
Find proteins for C1DK98 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DK98 
Go to UniProtKB:  C1DK98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DK98
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.124 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.97α = 90
b = 89.87β = 109.06
c = 59.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L011468/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-21
    Changes: Data collection