1SM4

Crystal Structure Analysis of the Ferredoxin-NADP+ Reductase from Paprika


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of paprika ferredoxin-NADP+ reductase. Implications for the electron transfer pathway.

Dorowski, A.Hofmann, A.Steegborn, C.Boicu, M.Huber, R.

(2001) J.Biol.Chem. 276: 9253-9263

  • DOI: 10.1074/jbc.M004576200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • cDNA of Capsicum annuum Yolo Wonder (paprika) has been prepared from total cellular RNA, and the complete gene encoding paprika ferredoxin-NADP(+) reductase (pFNR) precursor was sequenced and cloned from this cDNA. Fusion to a T7 promoter allowed exp ...

    cDNA of Capsicum annuum Yolo Wonder (paprika) has been prepared from total cellular RNA, and the complete gene encoding paprika ferredoxin-NADP(+) reductase (pFNR) precursor was sequenced and cloned from this cDNA. Fusion to a T7 promoter allowed expression in Escherichia coli. Both native and recombinant pFNR were purified to homogeneity and crystallized. The crystal structure of pFNR has been solved by Patterson search techniques using the structure of spinach ferredoxin-NADP(+) reductase as search model. The structure was refined at 2.5-A resolution to a crystallographic R-factor of 19.8% (R(free) = 26.5%). The overall structure of pFNR is similar to other members of the ferredoxin-NADP(+) reductase family, the major differences concern a long loop (residues 167-177) that forms part of the FAD binding site and some of the variable loops in surface regions. The different orientation of the FAD binding loop leads to a tighter interaction between pFNR and the adenine moiety of FAD. The physiological redox partners [2Fe-2S]-ferredoxin I and NADP(+) were modeled into the native structure of pFNR. The complexes reveal a protein-protein interaction site that is consistent with existing biochemical data and imply possible orientations for the side chain of tyrosine 362, which has to be displaced by the nicotinamide moiety of NADP(+) upon binding. A reasonable electron transfer pathway could be deduced from the modeled structures of the complexes.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, 82152 Planegg-Martinsried, Germany. anja.dorowski@gmx.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chloroplast ferredoxin-NADP+ oxidoreductase
A, B
296Capsicum annuumMutation(s): 0 
Gene Names: fnr
EC: 1.18.1.2
Find proteins for Q9M4D2 (Capsicum annuum)
Go to UniProtKB:  Q9M4D2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.720α = 90.00
b = 108.980β = 95.57
c = 90.360γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
CNSrefinement
ROTAVATAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description