5VW9

Nicotinamide soak of Y316S mutant of corn root ferredoxin:NADP+ reductase in alternate space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.135 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

High-resolution studies of hydride transfer in the ferredoxin:NADP(+) reductase superfamily.

Kean, K.M.Carpenter, R.A.Pandini, V.Zanetti, G.Hall, A.R.Faber, R.Aliverti, A.Karplus, P.A.

(2017) FEBS J 284: 3302-3319

  • DOI: https://doi.org/10.1111/febs.14190
  • Primary Citation of Related Structures:  
    5VW2, 5VW3, 5VW4, 5VW5, 5VW6, 5VW7, 5VW8, 5VW9, 5VWA, 5VWB

  • PubMed Abstract: 

    Ferredoxin: NADP + reductase (FNR) is an FAD-containing enzyme best known for catalysing the transfer of electrons from ferredoxin (Fd) to NADP + to make NADPH during photosynthesis. It is also the prototype for a broad enzyme superfamily, including the NADPH oxidases (NOXs) that all catalyse similar FAD-enabled electron transfers between NAD(P)H and one-electron carriers. Here, we define further mechanistic details of the NAD(P)H ⇌ FAD hydride-transfer step of the reaction based on spectroscopic studies and high-resolution (~ 1.5 Å) crystallographic views of the nicotinamide-flavin interaction in crystals of corn root FNR Tyr316Ser and Tyr316Ala variants soaked with either nicotinamide, NADP + , or NADPH. The spectra obtained from FNR crystal complexes match those seen in solution and the complexes reveal active site packing interactions and patterns of covalent distortion of the FAD that imply significant active site compression that would favour catalysis. Furthermore, anisotropic B-factors show that the mobility of the C4 atom of the nicotinamide in the FNR:NADP + complex has a directionality matching that expected for boat-like excursions of the nicotinamide ring thought to enhance hydride transfer. Arguments are made for the relevance of this binding mode to catalysis, and specific consideration is given to how the results extrapolate to provide insight to structure-function relations for the membrane-bound NOX enzymes for which little structural information has been available. Structural data are available in the PDB database under the accession numbers 3LO8 (wild-type), 5VW4 [Y316S:nicotinamide (P3 2 21)], 5VW9 [Y316S:nicotinamide (P3 1 21)], 5VW3 [Y316S:NADP + (P3 2 21)], 5VW8 [Y316S:NADP + (P3 1 21)], 5VW2 [Y316S:NADPH (P3 2 21)], 5VW5 [Y316A:nicotinamide (P3 2 21)], 5VW6 [Y316A:NADP + (P3 2 21)], 5VW7 [Y316A:NADPH (P3 2 21)], 5VWA [Y316F (P3 2 21)], and 5VWB [Y316F:NADP + (P3 1 21)]. Enzyme Commission number: ferredoxin:NADP + reductase - E C1.18.1.2.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--NADP reductase316Zea maysMutation(s): 1 
EC: 1.18.1.2
UniProt
Find proteins for B4G043 (Zea mays)
Explore B4G043 
Go to UniProtKB:  B4G043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4G043
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.135 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.9α = 90
b = 58.9β = 90
c = 184.407γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

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 StatesR01-GM119227
National Science Foundation (NSF, United States)United StatesMCB-9982727

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 1.2: 2017-10-11
    Changes: Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description