3D21 | pdb_00003d21

Crystal structure of a poplar wild-type thioredoxin h, PtTrxh4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

An Atypical Catalytic Mechanism Involving Three Cysteines of Thioredoxin.

Koh, C.S.Navrot, N.Didierjean, C.Rouhier, N.Hirasawa, M.Knaff, D.B.Wingsle, G.Samian, R.Jacquot, J.P.Corbier, C.Gelhaye, E.

(2008) J Biological Chem 283: 23062-23072

  • DOI: https://doi.org/10.1074/jbc.M802093200
  • Primary Citation Related Structures: 
    3D21, 3D22

  • PubMed Abstract: 

    Unlike other thioredoxins h characterized so far, a poplar thioredoxin of the h type, PtTrxh4, is reduced by glutathione and glutaredoxin (Grx) but not NADPH:thioredoxin reductase (NTR). PtTrxh4 contains three cysteines: one localized in an N-terminal extension (Cys(4)) and two (Cys(58) and Cys(61)) in the classical thioredoxin active site ((57)WCGPC(61)). The property of a mutant in which Cys(58) was replaced by serine demonstrates that it is responsible for the initial nucleophilic attack during the catalytic cycle. The observation that the C4S mutant is inactive in the presence of Grx but fully active when dithiothreitol is used as a reductant indicates that Cys(4) is required for the regeneration of PtTrxh4 by Grx. Biochemical and x-ray crystallographic studies indicate that two intramolecular disulfide bonds involving Cys(58) can be formed, linking it to either Cys(61) or Cys(4). We propose thus a four-step disulfide cascade mechanism involving the transient glutathionylation of Cys(4) to convert this atypical thioredoxin h back to its active reduced form.


  • Organizational Affiliation
    • Equipe Biocristallographie, UMR 7036 CNRS-Université Henri Poincaré, URAFPA, Equipe PB2P, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre Cedex France.

Macromolecule Content 

  • Total Structure Weight: 31.33 kDa 
  • Atom Count: 1,842 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 278 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thioredoxin H-type
A, B
139Populus trichocarpa x Populus deltoidesMutation(s): 0 
UniProt
Find proteins for P85801 (Populus jackii)
Explore P85801 
Go to UniProtKB:  P85801
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP85801
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.355α = 90
b = 47.355β = 90
c = 195.996γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary