8ENM

CryoEM structure of the high pH nitrogenase MoFe-protein under non-turnover conditions


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural consequences of turnover-induced homocitrate loss in nitrogenase.

Warmack, R.A.Maggiolo, A.O.Orta, A.Wenke, B.B.Howard, J.B.Rees, D.C.

(2023) Nat Commun 14: 1091-1091

  • DOI: https://doi.org/10.1038/s41467-023-36636-4
  • Primary Citation of Related Structures:  
    8CRS, 8DBX, 8ENL, 8ENM, 8ENN, 8ENO

  • PubMed Abstract: 

    Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA. rwarmack@caltech.edu.


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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS
Query on ICS

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF
Query on CLF

Download Ideal Coordinates CCD File 
G [auth B],
L [auth D]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA
Query on HCA

Download Ideal Coordinates CCD File 
F [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 
H [auth B],
K [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM045162
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143836-01
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection