6O7S | pdb_00006o7s

Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the indigo carmine oxidized state

  • Classification: OXIDOREDUCTASE
  • Organism(s): Azotobacter vinelandii
  • Mutation(s): Yes 

  • Deposited: 2019-03-08 Released: 2019-06-19 
  • Deposition Author(s): Rutledge, H.L., Tezcan, F.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6O7S

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Redox-Dependent Metastability of the Nitrogenase P-Cluster.

Rutledge, H.L.Rittle, J.Williamson, L.M.Xu, W.A.Gagnon, D.M.Tezcan, F.A.

(2019) J Am Chem Soc 141: 10091-10098

  • DOI: https://doi.org/10.1021/jacs.9b04555
  • Primary Citation Related Structures: 
    6O7L, 6O7M, 6O7N, 6O7O, 6O7P, 6O7Q, 6O7R, 6O7S

  • PubMed Abstract: 

    Molybdenum nitrogenase catalyzes the reduction of dinitrogen into ammonia, which requires the coordinated transfer of eight electrons to the active site cofactor (FeMoco) through the intermediacy of an [8Fe-7S] cluster (P-cluster), both housed in the molybdenum-iron protein (MoFeP). Previous studies on MoFeP from two different organisms, Azotobacter vinelandii ( Av) and Gluconacetobacter diazotrophicus ( Gd), have established that the P-cluster is conformationally flexible and can undergo substantial structural changes upon two-electron oxidation to the P OX state, whereby a backbone amidate and an oxygenic residue (Ser or Tyr) ligate to two of the cluster's Fe centers. This redox-dependent change in coordination has been implicated in the conformationally gated electron transfer in nitrogenase. Here, we have investigated the role of the oxygenic ligand in Av MoFeP, which natively contains a Ser ligand (βSer188) to the P-cluster. Three variants were generated in which (1) the oxygenic ligand was eliminated (βSer188Ala), (2) the P-cluster environment was converted to the one in Gd MoFeP (βPhe99Tyr/βSer188Ala), and (3) two oxygenic ligands were simultaneously included (βPhe99Tyr). Our studies have revealed that the P-cluster can become compositionally labile upon oxidation and reversibly lose one or two Fe centers in the absence of the oxygenic ligand, while still retaining wild-type-like dinitrogen reduction activity. Our findings also suggest that Av and Gd MoFePs evolved with specific preferences for Ser and Tyr ligands, respectively, and that the structural control of these ligands must extend beyond the primary and secondary coordination spheres of the P-cluster. The P-cluster adds to the increasing number of examples of inherently labile Fe-S clusters whose compositional instability may be an obligatory feature to enable redox-linked conformational changes to facilitate multielectron redox reactions.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0356 , United States.

Macromolecule Content 

  • Total Structure Weight: 233.03 kDa 
  • Atom Count: 17,147 
  • Modeled Residue Count: 1,996 
  • Deposited Residue Count: 2,030 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandiiMutation(s): 1 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS

Query on ICS



Download:Ideal Coordinates CCD File
F [auth A],
K [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
LPJ

Query on LPJ



Download:Ideal Coordinates CCD File
H [auth B],
M [auth D]
FE(6)-S(7) CLUSTER
Fe6 S7
KLKIXVGTRIXICL-UHFFFAOYSA-N
HCA

Query on HCA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
I [auth B],
N [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A],
L [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.775α = 90
b = 128.05β = 108.97
c = 107.539γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099813
Other privateUnited StatesHerman Frasch Foundation 735-HF12

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description