3AB1

Crystal Structure of Ferredoxin NADP+ Oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Asymmetric dimeric structure of ferredoxin-NAD(P)+ oxidoreductase from the green sulfur bacterium Chlorobaculum tepidum: implications for binding ferredoxin and NADP+

Muraki, N.Seo, D.Shiba, T.Sakurai, T.Kurisu, G.

(2010) J.Mol.Biol. 401: 403-414

  • DOI: 10.1016/j.jmb.2010.06.024

  • PubMed Abstract: 
  • Ferredoxin-NAD(P)(+) oxidoreductase (FNR) catalyzes the reduction of NAD(P)(+) to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum ...

    Ferredoxin-NAD(P)(+) oxidoreductase (FNR) catalyzes the reduction of NAD(P)(+) to NAD(P)H with the reduced ferredoxin (Fd) during the final step of the photosynthetic electron transport chain. FNR from the green sulfur bacterium Chlorobaculum tepidum is functionally analogous to plant-type FNR but shares a structural homology to NADPH-dependent thioredoxin reductase (TrxR). Here, we report the crystal structure of C. tepidum FNR to 2.4 A resolution, which reveals a unique structure-function relationship. C. tepidum FNR consists of two functional domains for binding FAD and NAD(P)H that form a homodimer in which the domains are arranged asymmetrically. One NAD(P)H domain is present as the open form, the other with the equivalent NAD(P)H domain as the relatively closed form. We used site-directed mutagenesis on the hinge region connecting the two domains in order to investigate the importance of the flexible hinge. The asymmetry of the NAD(P)H domain and the comparison with TrxR suggested that the hinge motion might be involved in pyridine nucleotide binding and binding of Fd. Surprisingly, the crystal structure revealed an additional C-terminal sub-domain that tethers one protomer and interacts with the other protomer by pi-pi stacking of Phe337 and the isoalloxazine ring of FAD. The position of this stacking Phe337 is almost identical with both of the conserved C-terminal Tyr residues of plant-type FNR and the active site dithiol of TrxR, implying a unique structural basis for enzymatic reaction of C. tepidum FNR.


    Organizational Affiliation

    Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin--NADP reductase
A, B
360Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)Mutation(s): 0 
EC: 1.18.1.2
Find proteins for Q8KCB2 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Go to UniProtKB:  Q8KCB2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 2.39 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.240 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 100.514α = 90.00
b = 127.971β = 90.00
c = 128.353γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data scaling
ADSCdata collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance