5JCA | pdb_00005jca

NADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb5JCA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrococcus furiosus
• Mutation(s): No 


• Deposited: 2016-04-14 Released: 2017-04-12 
• Deposition Author(s): Zadvornyy, O.A., Schut, G.J., Nguyen, D.M., Artz, J.H., Tokmina-Lukaszewska, M., Lipscomb, G., Adams, M.W., Peters, J.W.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.153 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Mechanistic insights into energy conservation by flavin-based electron bifurcation.

Lubner, C.E., Jennings, D.P., Mulder, D.W., Schut, G.J., Zadvornyy, O.A., Hoben, J.P., Tokmina-Lukaszewska, M., Berry, L., Nguyen, D.M., Lipscomb, G.L., Bothner, B., Jones, A.K., Miller, A.F., King, P.W., Adams, M.W.W., Peters, J.W.

(2017) Nat Chem Biol 13: 655-659

• PubMed: 28394885 
• DOI: https://doi.org/10.1038/nchembio.2348
• Primary Citation Related Structures: 
  5JCA, 5JFC


• PubMed Abstract: 
  

  The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. The unprecedented range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.

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Organizational Affiliation: 
• Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA.
Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA.
Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.67 kDa 
• Atom Count: 7,072 
• Modeled Residue Count: 750 
• Deposited Residue Count: 758 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha	A [auth L]	474	Pyrococcus furiosus	Mutation(s): 0  EC: 1.6.1.4 (PDB Primary Data), 1.18.1.2 (UniProt), 1.8.1.19 (UniProt)
UniProt
Find proteins for Q8U195 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U195  Go to UniProtKB:  Q8U195

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta	B [auth S]	284	Pyrococcus furiosus	Mutation(s): 0  EC: 1.6.1.4 (PDB Primary Data), 1.18.1.2 (UniProt), 1.8.1.19 (UniProt)
UniProt
Find proteins for Q8U194 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U194  Go to UniProtKB:  Q8U194

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth L], H [auth S]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP	F [auth L]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SF4	C [auth L], D [auth L]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	I [auth S]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	G [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	J [auth S]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.153 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.681	α = 90
b = 179.681	β = 90
c = 80.672	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Zadvornyy, O.A., Schut, G.J., Nguyen, D.M., Artz, J.H., Tokmina-Lukaszewska, M., Lipscomb, G., Adams, M.W., Peters, J.W.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0012518

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2017-05-31
  Changes: Database references
• Version 1.3: 2022-03-16
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection