5JCA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/nchembio.2348
  • Structures With Same Primary Citation

  • 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 oxi ...

    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.


    Organizational Affiliation

    Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit alpha
L
474Pyrococcus furiosusMutation(s): 0 
EC: 1.6.1.4 (PDB Primary Data), 1.8.1.19 (UniProt), 1.18.1.2 (UniProt)
Find proteins for Q8U195 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U195
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) subunit beta
S
284Pyrococcus furiosusMutation(s): 0 
EC: 1.6.1.4 (PDB Primary Data), 1.8.1.19 (UniProt), 1.18.1.2 (UniProt)
Find proteins for Q8U194 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U194
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
L, S
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NDP
Query on NDP

Download CCD File 
L
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
L
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download CCD File 
S
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.681α = 90
b = 179.681β = 90
c = 80.672γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
US Department of Energy, Office of ScienceUnited StatesDE-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