5VJ7

Ferredoxin NADP Oxidoreductase (Xfn)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Two functionally distinct NADP(+)-dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus.

Nguyen, D.M.N.Schut, G.J.Zadvornyy, O.A.Tokmina-Lukaszewska, M.Poudel, S.Lipscomb, G.L.Adams, L.A.Dinsmore, J.T.Nixon, W.J.Boyd, E.S.Bothner, B.Peters, J.W.Adams, M.W.W.

(2017) J Biol Chem 292: 14603-14616

  • DOI: https://doi.org/10.1074/jbc.M117.794172
  • Primary Citation of Related Structures:  
    5VJ7

  • PubMed Abstract: 

    Electron bifurcation has recently gained acceptance as the third mechanism of energy conservation in which energy is conserved through the coupling of exergonic and endergonic reactions. A structure-based mechanism of bifurcation has been elucidated recently for the flavin-based enzyme NADH-dependent ferredoxin NADP + oxidoreductase I (NfnI) from the hyperthermophillic archaeon Pyrococcus furiosus. NfnI is thought to be involved in maintaining the cellular redox balance, producing NADPH for biosynthesis by recycling the two other primary redox carriers, NADH and ferredoxin. The P. furiosus genome encodes an NfnI paralog termed NfnII, and the two are differentially expressed, depending on the growth conditions. In this study, we show that deletion of the genes encoding either NfnI or NfnII affects the cellular concentrations of NAD(P)H and particularly NADPH. This results in a moderate to severe growth phenotype in deletion mutants, demonstrating a key role for each enzyme in maintaining redox homeostasis. Despite their similarity in primary sequence and cofactor content, crystallographic, kinetic, and mass spectrometry analyses reveal that there are fundamental structural differences between the two enzymes, and NfnII does not catalyze the NfnI bifurcating reaction. Instead, it exhibits non-bifurcating ferredoxin NADP oxidoreductase-type activity. NfnII is therefore proposed to be a bifunctional enzyme and also to catalyze a bifurcating reaction, although its third substrate, in addition to ferredoxin and NADP(H), is as yet unknown.


  • Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase476Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_09035
UniProt
Find proteins for I6V148 (Pyrococcus furiosus COM1)
Explore I6V148 
Go to UniProtKB:  I6V148
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6V148
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-NADP(+) reductase subunit alpha289Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: PFC_09030
EC: 1.18.1.2
UniProt
Find proteins for I6TYZ3 (Pyrococcus furiosus COM1)
Explore I6TYZ3 
Go to UniProtKB:  I6TYZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6TYZ3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.743α = 90
b = 73.14β = 96.73
c = 99.963γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0012518

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2017-09-20
    Changes: Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description