2VM2

Crystal structure of barley thioredoxin h isoform 1 crystallized using PEG as precipitant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of Barley Thioredoxin H Isoforms Hvtrxh1 and Hvtrxh2 Reveal Features Involved in Protein Recognition and Possibly in Discriminating the Isoform Specificity.

Maeda, K.Hagglund, P.Finnie, C.Svensson, B.Henriksen, A.

(2008) Protein Sci 17: 1015

  • DOI: https://doi.org/10.1110/ps.083460308
  • Primary Citation of Related Structures:  
    2VLT, 2VLU, 2VLV, 2VM1, 2VM2

  • PubMed Abstract: 

    H-type thioredoxins (Trxs) constitute a particularly large Trx sub-group in higher plants. Here, the crystal structures are determined for the two barley Trx h isoforms, HvTrxh1 and HvTrxh2, in the partially radiation-reduced state to resolutions of 1.7 A, and for HvTrxh2 in the oxidized state to 2.0 A. The two Trxs have a sequence identity of 51% and highly similar fold and active-site architecture. Interestingly, the four independent molecules in the crystals of HvTrxh1 form two relatively large and essentially identical protein-protein interfaces. In each interface, a loop segment of one HvTrxh1 molecule is positioned along a shallow hydrophobic groove at the primary nucleophile Cys40 of another HvTrxh1 molecule. The association mode can serve as a model for the target protein recognition by Trx, as it brings the Met82 Cgamma atom (gamma position as a disulfide sulfur) of the bound loop segment in the proximity of the Cys40 thiol. The interaction involves three characteristic backbone-backbone hydrogen bonds in an antiparallel beta-sheet-like arrangement, similar to the arrangement observed in the structure of an engineered, covalently bound complex between Trx and a substrate protein, as reported by Maeda et al. in an earlier paper. The occurrence of an intermolecular salt bridge between Glu80 of the bound loop segment and Arg101 near the hydrophobic groove suggests that charge complementarity plays a role in the specificity of Trx. In HvTrxh2, isoleucine corresponds to this arginine, which emphasizes the potential for specificity differences between the coexisting barley Trx isoforms.


  • Organizational Affiliation

    Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOREDOXIN H ISOFORM 1.
A, B, C, D
118Hordeum vulgare subsp. vulgareMutation(s): 0 
EC: 1.8.1.9
UniProt
Find proteins for Q7XZK3 (Hordeum vulgare subsp. vulgare)
Explore Q7XZK3 
Go to UniProtKB:  Q7XZK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7XZK3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.726α = 90
b = 33.663β = 112.48
c = 132.202γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Other
  • Version 1.3: 2017-07-12
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description