5N6Y

Azotobacter vinelandii vanadium nitrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.109 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The structure of vanadium nitrogenase reveals an unusual bridging ligand.

Sippel, D.Einsle, O.

(2017) Nat. Chem. Biol. 13: 956-960

  • DOI: 10.1038/nchembio.2428

  • PubMed Abstract: 
  • Nitrogenases catalyze the reduction of dinitrogen (N2) gas to ammonium at a complex heterometallic cofactor. This most commonly occurs at the FeMo cofactor (FeMoco), a [Mo-7Fe-9S-C] cluster whose exact reactivity and substrate-binding mode remain unk ...

    Nitrogenases catalyze the reduction of dinitrogen (N2) gas to ammonium at a complex heterometallic cofactor. This most commonly occurs at the FeMo cofactor (FeMoco), a [Mo-7Fe-9S-C] cluster whose exact reactivity and substrate-binding mode remain unknown. Alternative nitrogenases replace molybdenum with either vanadium or iron and differ in reactivity, most prominently in the ability of vanadium nitrogenase to reduce CO to hydrocarbons. Here we report the 1.35-Å structure of vanadium nitrogenase from Azotobacter vinelandii. The 240-kDa protein contains an additional α-helical subunit that is not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V-7Fe-8S-C] cluster with a homocitrate ligand to vanadium. Unexpectedly, it lacks one sulfide ion compared to FeMoco, which is replaced by a bridging ligand, likely a μ-1,3-carbonate. The anion fits into a pocket within the protein that is obstructed in molybdenum nitrogenase, and its different chemical character helps to rationalize the altered chemical properties of this unique N2- and CO-fixing enzyme.


    Organizational Affiliation

    Lehrstuhl Biochemie, Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg Research Institute for Advanced Studies (FRIAS), and BIOSS Centre for Biological Signalling Studies, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase vanadium-iron protein alpha chain
A, D
474Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfD
EC: 1.18.6.1
Find proteins for P16855 (Azotobacter vinelandii)
Go to UniProtKB:  P16855
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase vanadium-iron protein beta chain
E, B
475Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfK
EC: 1.18.6.1
Find proteins for P16856 (Azotobacter vinelandii)
Go to UniProtKB:  P16856
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase vanadium-iron protein delta chain
C, F
113Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfG
EC: 1.18.6.1
Find proteins for P16857 (Azotobacter vinelandii)
Go to UniProtKB:  P16857
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8P8
Query on 8P8

Download SDF File 
Download CCD File 
A, D
C Fe7 S8 V
C Fe7 S8 V
DYVZWQKCGNUCRR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A, D
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
CLF
Query on CLF

Download SDF File 
Download CCD File 
A, E
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
 Ligand Interaction
HCA
Query on HCA

Download SDF File 
Download CCD File 
A, D
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.109 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 75.250α = 84.06
b = 79.790β = 72.62
c = 106.970γ = 75.15
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-16 
  • Released Date: 2017-07-26 
  • Deposition Author(s): Sippel, D., Einsle, O.

Funding OrganizationLocationGrant Number
European Research CouncilGermany310656
German Research FoundationGermanyRTG 1976
German Research FoundationGermanyEI-520/10

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references
  • Version 2.0: 2017-09-20
    Type: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence