6O0B

Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and Mechanistic Insights into CO2Activation by Nitrogenase Iron Protein.

Rettberg, L.A.Stiebritz, M.T.Kang, W.Lee, C.C.Ribbe, M.W.Hu, Y.

(2019) Chemistry 25: 13078-13082

  • DOI: https://doi.org/10.1002/chem.201903387
  • Primary Citation of Related Structures:  
    6O0B

  • PubMed Abstract: 

    The Fe protein of nitrogenase catalyzes the ambient reduction of CO 2 when its cluster is present in the all-ferrous, [Fe 4 S 4 ] 0 oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO 2 . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe 4 S 4 ] 0 and [Fe 4 S 4 ] + states point to a possible asymmetric functionality of a highly conserved Arg pair in CO 2 binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO 2 activation by a surface-exposed, scaffold-held [Fe 4 S 4 ] cluster.


  • Organizational Affiliation

    Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697-3900, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein
A, B
289Azotobacter vinelandii DJMutation(s): 0 
Gene Names: nifHAvin_01380
EC: 1.18.6.1
UniProt
Find proteins for C1DGZ6 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303))
Explore C1DGZ6 
Go to UniProtKB:  C1DGZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1DGZ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.071α = 90
b = 93.045β = 98.875
c = 60.796γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1651398

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description