6VXT

Activated Nitrogenase MoFe-protein from Azotobacter vinelandii

  • Classification: OXIDOREDUCTASE
  • Organism(s): Azotobacter vinelandii
  • Mutation(s): No 

  • Deposited: 2020-02-24 Released: 2020-06-24 
  • Deposition Author(s): Kang, W., Hu, Y., Ribbe, M.W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Structural evidence for a dynamic metallocofactor during N2reduction by Mo-nitrogenase.

Kang, W.Lee, C.C.Jasniewski, A.J.Ribbe, M.W.Hu, Y.

(2020) Science 368: 1381-1385

  • DOI: https://doi.org/10.1126/science.aaz6748
  • Primary Citation of Related Structures:  
    6UG0, 6VXT

  • PubMed Abstract: 

    The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo-O5 (carboxyl) or Mo-O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07328 (Azotobacter vinelandii)
Explore P07328 
Go to UniProtKB:  P07328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07328
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandiiMutation(s): 0 
EC: 1.18.6.1
UniProt
Find proteins for P07329 (Azotobacter vinelandii)
Explore P07329 
Go to UniProtKB:  P07329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07329
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS (Subject of Investigation/LOI)
Query on ICS

Download Ideal Coordinates CCD File 
F [auth A],
T [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF (Subject of Investigation/LOI)
Query on CLF

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L [auth A],
Y [auth C]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA
Query on HCA

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E [auth A],
S [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
MO
Query on MO

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G [auth A]
H [auth A]
J [auth A]
K [auth A]
U [auth C]
G [auth A],
H [auth A],
J [auth A],
K [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth D]
BA [auth D]
CA [auth D]
N [auth B]
O [auth B]
AA [auth D],
BA [auth D],
CA [auth D],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

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M [auth B],
R [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
H2S
Query on H2S

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I [auth A],
Z [auth D]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.535α = 90
b = 203.435β = 103.945
c = 83.857γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM67626
Department of Energy (DOE, United States)United StatesDE-SC0016510

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description