5G30

Crystallographic structure of mutant D60S of thioredoxin from Litopenaeus vannamei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.

Campos-Acevedo, A.A.Sotelo-Mundo, R.R.Perez, J.Rudino-Pinera, E.

(2017) Acta Crystallogr D Struct Biol 73: 326-339

  • DOI: https://doi.org/10.1107/S2059798317002066
  • Primary Citation of Related Structures:  
    5G2Z, 5G30, 5G31

  • PubMed Abstract: 

    The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo. Crystallographic data for shrimp thioredoxin (LvTrx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx. Through the analysis of five mutants located at the crystallographic interface, this study provides structural and biochemical evidence for the existence in solution of monomeric and dimeric populations of wild-type LvTrx and five mutants. Based on the results of biochemical assays, SAXS studies and the crystallographic structures of three of the studied mutants (Cys73Ser, Asp60Ser and Trp31Ala), it is clear that the Cys73 residue is essential for dimerization. However, its mutation to Ser produces an enzyme which has similar redox activity in vitro to the wild type. A putative regulatory function of dimerization is proposed based on structural analysis. Nonetheless, the biological role of LvTrx dimerization needs to be experimentally unveiled. Additionally, the findings of this work reopen the discussion regarding the existence of similar behaviour in human thioredoxin, which shares a Cys at position 73 with LvTrx, a structural feature that is also present in some Trxs from vertebrates and crustaceans.


  • Organizational Affiliation

    Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, 62210 Cuernavaca, MOR, Mexico.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOREDOXIN
A, B, C, D
105Penaeus vannameiMutation(s): 1 
EC: 1.8.1.9
UniProt
Find proteins for B1PWB9 (Penaeus vannamei)
Explore B1PWB9 
Go to UniProtKB:  B1PWB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1PWB9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.491α = 90
b = 82.712β = 102.58
c = 82.206γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description