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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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
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:  (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
Expand
  • 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

View Full Validation Report



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