2VNJ

X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM I AT 2.13 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coenzyme Binding and Hydride Transfer in Rhodobacter Capsulatus Ferredoxin/Flavodoxin Nadp(H) Oxidoreductase.

Bortolotti, A.Perez-Dorado, I.Goni, G.Medina, M.Hermoso, J.A.Carrillo, N.Cortez, N.

(2009) Biochim.Biophys.Acta 1794: 199

  • DOI: 10.1016/j.bbapap.2008.09.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferredoxin-NADP(H) reductases catalyse the reversible hydride/electron exchange between NADP(H) and ferredoxin/flavodoxin, comprising a structurally defined family of flavoenzymes with two distinct subclasses. Those present in Gram-negative bacteria ...

    Ferredoxin-NADP(H) reductases catalyse the reversible hydride/electron exchange between NADP(H) and ferredoxin/flavodoxin, comprising a structurally defined family of flavoenzymes with two distinct subclasses. Those present in Gram-negative bacteria (FPRs) display turnover numbers of 1-5 s(-1) while the homologues of cyanobacteria and plants (FNRs) developed a 100-fold activity increase. We investigated nucleotide interactions and hydride transfer in Rhodobacter capsulatus FPR comparing them to those reported for FNRs. NADP(H) binding proceeds as in FNRs with stacking of the nicotinamide on the flavin, which resulted in formation of charge-transfer complexes prior to hydride exchange. The affinity of FPR for both NADP(H) and 2'-P-AMP was 100-fold lower than that of FNRs. The crystal structure of FPR in complex with 2'-P-AMP and NADP(+) allowed modelling of the adenosine ring system bound to the protein, whereas the nicotinamide portion was either not visible or protruding toward solvent in different obtained crystals. Stabilising contacts with the active site residues are different in the two reductase classes. We conclude that evolution to higher activities in FNRs was partially favoured by modification of NADP(H) binding in the initial complexes through changes in the active site residues involved in stabilisation of the adenosine portion of the nucleotide and in the mobile C-terminus of FPR.


    Related Citations: 
    • 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
    • The Feredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus: Molecular Structure and Catalytic Mechanism
      Nogues, I.,Perez-Dorado, I.,Frago, S.,Bittel, C.,Mayhew, S.,Gomez-Moreno, C.,Hermoso, J.A.,Medina, M.,Cortez, N.,Carrillo, N.
      (2005) Biochemistry 44: 11730
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Ferredoxin-Nadp(H) Reductase from Rhodobacter Capsulatus
      Perez-Dorado, I.,Bittel, C.,Cortez, N.,Hermoso, J.A.
      (2004) Acta Crystallogr.,Sect.D 60: 2332


    Organizational Affiliation

    Instituto de BiologĂ­a Molecular y Celular de Rosario, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH\:FERREDOXIN REDUCTASE
A
272Rhodobacter capsulatusMutation(s): 0 
Gene Names: fpr
EC: 1.18.1.2, 1.19.1.1
Find proteins for Q9L6V3 (Rhodobacter capsulatus)
Go to UniProtKB:  Q9L6V3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HTG
Query on HTG

Download SDF File 
Download CCD File 
A
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKd: 222000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.720α = 90.00
b = 68.720β = 90.00
c = 128.150γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance