8BTS

Nitrogenase MoFe protein from A. vinelandii alpha double mutant C45A/L158C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Nitrogen Fixation and Hydrogen Evolution by Sterically Encumbered Mo-Nitrogenase.

Cadoux, C.Ratcliff, D.Maslac, N.Gu, W.Tsakoumagkos, I.Hoogendoorn, S.Wagner, T.Milton, R.D.

(2023) JACS Au 3: 1521-1533

  • DOI: https://doi.org/10.1021/jacsau.3c00165
  • Primary Citation of Related Structures:  
    8BTS

  • PubMed Abstract: 

    The substrate-reducing proteins of all nitrogenases (MoFe, VFe, and FeFe) are organized as α 2 ß 2 2 ) multimers with two functional halves. While their dimeric organization could afford improved structural stability of nitrogenases in vivo , previous research has proposed both negative and positive cooperativity contributions with respect to enzymatic activity. Here, a 1.4 kDa peptide was covalently introduced in the proximity of the P cluster, corresponding to the Fe protein docking position. The Strep-tag carried by the added peptide simultaneously sterically inhibits electron delivery to the MoFe protein and allows the isolation of partially inhibited MoFe proteins (where the half-inhibited MoFe protein was targeted). We confirm that the partially functional MoFe protein retains its ability to reduce N 2 to NH 3 , with no significant difference in selectivity over obligatory/parasitic H 2 formation. Our experiment concludes that wild-type nitrogenase exhibits negative cooperativity during the steady state regarding H 2 and NH 3 formation (under Ar or N 2 ), with one-half of the MoFe protein inhibiting turnover in the second half. This emphasizes the presence and importance of long-range (>95 Å) protein-protein communication in biological N 2 fixation in Azotobacter vinelandii .


  • Organizational Affiliation

    Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase protein alpha chainA,
C,
E [auth H],
G [auth J]
500Azotobacter vinelandii DJMutation(s): 2 
Gene Names: nifD
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 chainB,
D,
F [auth I],
H [auth L]
523Azotobacter vinelandii DJMutation(s): 0 
Gene Names: nifK
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
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS (Subject of Investigation/LOI)
Query on ICS

Download Ideal Coordinates CCD File 
GA [auth H],
J [auth A],
MA [auth J],
X [auth C]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
1CL (Subject of Investigation/LOI)
Query on 1CL

Download Ideal Coordinates CCD File 
AA [auth D],
IA [auth I],
N [auth B],
PA [auth L]
FE(8)-S(7) CLUSTER, OXIDIZED
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA (Subject of Investigation/LOI)
Query on HCA

Download Ideal Coordinates CCD File 
FA [auth H],
I [auth A],
LA [auth J],
W [auth C]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D]
HA [auth H]
JA [auth I]
M [auth A]
OA [auth J]
DA [auth D],
HA [auth H],
JA [auth I],
M [auth A],
OA [auth J],
RA [auth L],
SA [auth L],
T [auth B],
U [auth B],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
K [auth A]
L [auth A]
NA [auth J]
BA [auth D],
CA [auth D],
K [auth A],
L [auth A],
NA [auth J],
O [auth B],
P [auth B],
Q [auth B],
QA [auth L],
R [auth B],
S [auth B],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
EA [auth D],
KA [auth I],
TA [auth L],
V [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.392α = 90
b = 73.444β = 104.76
c = 211.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland180544
Swiss National Science FoundationSwitzerlandSNSF 310030_189246
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyWA 4053/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection