Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 32.29 kDa 
• Atom Count: 2416 
• Modelled Residue Count: 257 
• Deposited Residue Count: 272 
• Unique protein chains: 1

2BGI

X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus complexed with three molecules of the detergent n-heptyl- beta-D-thioglucoside at 1.7 Angstroms

• PDB DOI: 10.2210/pdb2BGI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodobacter capsulatus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-12-23 Released: 2005-09-07 
• Deposition Author(s): Perez-Dorado, J.I., Hermoso, J.A., Nogues, I., Frago, S., Bittel, C., Mayhew, S.G., Gomez-Moreno, C., Medina, M., Cortez, N., Carrillo, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.225 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

The Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism

Nogues, I., Perez-Dorado, J.I., Frago, S., Bittel, C., Mayhew, S.G., Gomez-Moreno, C., Hermoso, J.A., Medina, M., Cortez, N., Carrillo, N.

(2005) Biochemistry 44: 11730

• PubMed: 16128574 
• DOI: 10.1021/bi0508183
• Primary Citation of Related Structures:  
  2BGI, 2BGJ


• PubMed Abstract: 
  

The photosynthetic bacterium Rhodobacter capsulatus contains a ferredoxin (flavodoxin)-NADP(H) oxidoreductase (FPR) that catalyzes electron transfer between NADP(H) and ferredoxin or flavodoxin. The structure of the enzyme, determined by X-ray crystallography, contains two domains harboring the FAD and NADP(H) binding sites, as is typical of the FPR structural family. The FAD molecule is in a hairpin conformation in which stacking interactions can be established between the dimethylisoalloxazine and adenine moieties. The midpoint redox potentials of the various transitions undergone by R. capsulatus FPR were similar to those reported for their counterparts involved in oxygenic photosynthesis, but its catalytic activity is orders of magnitude lower (1-2 s(-)(1) versus 200-500 s(-)(1)) as is true for most of its prokaryotic homologues. To identify the mechanistic basis for the slow turnover in the bacterial enzymes, we dissected the R. capsulatus FPR reaction into hydride transfer and electron transfer steps, and determined their rates using stopped-flow methods. Hydride exchange between the enzyme and NADP(H) occurred at 30-150 s(-)(1), indicating that this half-reaction does not limit FPR activity. In contrast, electron transfer to flavodoxin proceeds at 2.7 s(-)(1), in the range of steady-state catalysis. Flavodoxin semiquinone was a better electron acceptor for FPR than oxidized flavodoxin under both single turnover and steady-state conditions. The results indicate that one-electron reduction of oxidized flavodoxin limits the enzyme activity in vitro, and support the notion that flavodoxin oscillates between the semiquinone and fully reduced states when FPR operates in vivo.

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Related Citations: 

• Crystallization and Preliminary X-Ray Diffraction Analysis of Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus
  Perez-Dorado, J.I., Bittel, C., Cortez, N., Hermoso, J.A.
  (2004) Acta Crystallogr D Biol Crystallogr 60: 2332

• The Oxidant-Responsive Diaphorase of Rhodobacter Capsulatus is a Ferredoxin (Flavodoxin)-Nadp(H) Reductase
  Bittel, C., Tabares, L.C., Armesto, M., Carrillo, N., Cortez, N.
  (2003) FEBS Lett 553: 408

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Organizational Affiliation: 

Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERREDOXIN-NADP(H) REDUCTASE	A	272	Rhodobacter capsulatus	Mutation(s): 0  Gene Names: fpr EC: 1.18.1.2 (PDB Primary Data), 1.19.1.1 (UniProt)
UniProt
Find proteins for Q9L6V3 (Rhodobacter capsulatus) Explore Q9L6V3  Go to UniProtKB:  Q9L6V3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HTG	C [auth A], D [auth A], F [auth A]	heptyl 1-thio-beta-D-glucopyranoside C13 H26 O5 S HPEGNLMTTNTJSP-LBELIVKGSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO2	G [auth A], H [auth A]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.225 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.848	α = 90
b = 120.848	β = 90
c = 50.709	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-23 
• Released Date: 2005-09-07 
Deposition Author(s): Perez-Dorado, J.I., Hermoso, J.A., Nogues, I., Frago, S., Bittel, C., Mayhew, S.G., Gomez-Moreno, C., Medina, M., Cortez, N., Carrillo, N.

Revision History  

• Version 1.0: 2005-09-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Other, Structure summary