2PVO | pdb_00002pvo

Crystal srtucture of the ternary complex between thioredoxin f, ferredoxin, and ferredoxin: thioredoxin reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.263 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.191 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2PVO

This is version 1.5 of the entry. See complete history

Literature

Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase.

Dai, S.Friemann, R.Glauser, D.A.Bourquin, F.Manieri, W.Schurmann, P.Eklund, H.

(2007) Nature 448: 92-96

  • DOI: https://doi.org/10.1038/nature05937
  • Primary Citation Related Structures: 
    2PU9, 2PUK, 2PUO, 2PVD, 2PVG, 2PVO

  • PubMed Abstract: 

    Oxygen-evolving photosynthetic organisms regulate carbon metabolism through a light-dependent redox signalling pathway. Electrons are shuttled from photosystem I by means of ferredoxin (Fdx) to ferredoxin-thioredoxin reductase (FTR), which catalyses the two-electron-reduction of chloroplast thioredoxins (Trxs). These modify target enzyme activities by reduction, regulating carbon flow. FTR is unique in its use of a [4Fe-4S] cluster and a proximal disulphide bridge in the conversion of a light signal into a thiol signal. We determined the structures of FTR in both its one- and its two-electron-reduced intermediate states and of four complexes in the pathway, including the ternary Fdx-FTR-Trx complex. Here we show that, in the first complex (Fdx-FTR) of the pathway, the Fdx [2Fe-2S] cluster is positioned suitably for electron transfer to the FTR [4Fe-4S] centre. After the transfer of one electron, an intermediate is formed in which one sulphur atom of the FTR active site is free to attack a disulphide bridge in Trx and the other sulphur atom forms a fifth ligand for an iron atom in the FTR [4Fe-4S] centre--a unique structure in biology. Fdx then delivers a second electron that cleaves the FTR-Trx heterodisulphide bond, which occurs in the Fdx-FTR-Trx complex. In this structure, the redox centres of the three proteins are aligned to maximize the efficiency of electron transfer from the Fdx [2Fe-2S] cluster to the active-site disulphide of Trxs. These results provide a structural framework for understanding the mechanism of disulphide reduction by an iron-sulphur enzyme and describe previously unknown interaction networks for both Fdx and Trx (refs 4-6).


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Integrated Department of Immunology, National Jewish Medical and Research Center & University of Colorado Health Sciences Center, 1400 Jackson Street, Denver, Colorado 80206, USA. dais@njc.org

Macromolecule Content 

  • Total Structure Weight: 44.33 kDa 
  • Atom Count: 3,071 
  • Modeled Residue Count: 391 
  • Deposited Residue Count: 391 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase, catalytic chain110Synechocystis sp.Mutation(s): 0 
Gene Names: ftrC
EC: 1.8.7.2
UniProt
Find proteins for Q55389 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q55389 
Go to UniProtKB:  Q55389
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55389
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-thioredoxin reductase, variable chain74Synechocystis sp.Mutation(s): 0 
Gene Names: ftrV
UniProt
Find proteins for Q55781 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q55781 
Go to UniProtKB:  Q55781
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55781
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin F-type, chloroplast111Spinacia oleraceaMutation(s): 1 
UniProt
Find proteins for P09856 (Spinacia oleracea)
Explore P09856 
Go to UniProtKB:  P09856
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09856
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ferredoxin-196Synechocystis sp.Mutation(s): 0 
Gene Names: petFfed
UniProt
Find proteins for P27320 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P27320 
Go to UniProtKB:  P27320
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27320
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.263 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.191 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.426α = 90
b = 130.426β = 90
c = 63.837γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2007-07-10 
  • Deposition Author(s): Dai, S.

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Data collection, Structure summary