6O7S

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

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

  • 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 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jacs.9b04555
  • Primary Citation of Related Structures:  

  • 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 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase molybdenum-iron protein alpha chain
A, C
492Azotobacter vinelandiiMutation(s): 0 
Gene Names: nifD
EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii)
Go to UniProtKB:  P07328
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrogenase molybdenum-iron protein beta chain
B, D
523Azotobacter vinelandiiMutation(s): 1 
Gene Names: nifK
EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii)
Go to UniProtKB:  P07329
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LPJ
Query on LPJ

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Download CCD File 
B, D
FE(6)-S(7) CLUSTER
Fe6 S7
KLKIXVGTRIXICL-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
B, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
ICS
Query on ICS

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Download CCD File 
A, C
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
 Ligand Interaction
HCA
Query on HCA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.775α = 90.00
b = 128.050β = 108.97
c = 107.539γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence