5CX1

Nitrogenase molybdenum-iron protein beta-K400E mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis.

Owens, C.P.Katz, F.E.Carter, C.H.Luca, M.A.Tezcan, F.A.

(2015) J Am Chem Soc 137: 12704-12712

  • DOI: https://doi.org/10.1021/jacs.5b08310
  • Primary Citation of Related Structures:  
    5CX1

  • PubMed Abstract: 

    Nitrogenase is the only enzyme that can convert atmospheric dinitrogen (N2) into biologically usable ammonia (NH3). To achieve this multielectron redox process, the nitrogenase component proteins, MoFe-protein (MoFeP) and Fe-protein (FeP), repeatedly associate and dissociate in an ATP-dependent manner, where one electron is transferred from FeP to MoFeP per association. Here, we provide experimental evidence that encounter complexes between FeP and MoFeP play a functional role in nitrogenase catalysis. The encounter complexes are stabilized by electrostatic interactions involving a positively charged patch on the β-subunit of MoFeP. Three single mutations (βAsn399Glu, βLys400Glu, and βArg401Glu) in this patch were generated in Azotobacter vinelandii MoFeP. All of the resulting variants displayed decreases in specific catalytic activity, with the βK400E mutation showing the largest effect. As simulated by the Thorneley-Lowe kinetic scheme, this single mutation lowered the rate constant for FeP-MoFeP association 5-fold. We also found that the βK400E mutation did not affect the coupling of ATP hydrolysis with electron transfer (ET) between FeP and MoFeP. These data suggest a mechanism where FeP initially forms encounter complexes on the MoFeP β-subunit surface en route to the ATP-activated, ET-competent complex over the αβ-interface.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92039, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein alpha chain
A, C, E, G, I
A, C, E, G, I, K, M, O
480Azotobacter 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase molybdenum-iron protein beta chain
B, D, F, H, J
B, D, F, H, J, L, N, P
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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ICS
Query on ICS

Download Ideal Coordinates CCD File 
DA [auth G]
HA [auth I]
LA [auth K]
PA [auth M]
R [auth A]
DA [auth G],
HA [auth I],
LA [auth K],
PA [auth M],
R [auth A],
TA [auth O],
V [auth C],
Z [auth E]
iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF
Query on CLF

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth G]
IA [auth I]
MA [auth K]
QA [auth M]
AA [auth E],
EA [auth G],
IA [auth I],
MA [auth K],
QA [auth M],
S [auth A],
UA [auth O],
W [auth C]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA
Query on HCA

Download Ideal Coordinates CCD File 
CA [auth G]
GA [auth I]
KA [auth K]
OA [auth M]
Q [auth A]
CA [auth G],
GA [auth I],
KA [auth K],
OA [auth M],
Q [auth A],
SA [auth O],
U [auth C],
Y [auth E]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth F]
FA [auth H]
JA [auth J]
NA [auth L]
RA [auth N]
BA [auth F],
FA [auth H],
JA [auth J],
NA [auth L],
RA [auth N],
T [auth B],
VA [auth P],
X [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.502α = 90
b = 144.595β = 114.27
c = 177.747γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection

Structure Validation

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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
United States Department of Agriculture (USDA)United States2015-67012-22895

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2018-08-29
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description