4L0U

Crystal structure of Plasmodium vivax Prx1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 2H66 - determined by Wernimont, A.K., Dong, A., Zhao, Y., Lew, J., Melone, M., Kozieradzki, I., Weigelt, J., Sundstrom, M., Edwards, A.M., Arrowsmith, C.H., Bochkarev, A., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)  

Literature

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag.

Gretes, M.C.Karplus, P.A.

(2013) Protein Sci. 22: 1445-1452

  • DOI: 10.1002/pro.2328
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the huma ...

    Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1a(N*) that has seven native N-terminal residues replaced by an affinity tag. This N-terminal modification disrupts a previously unrecognized, hydrophobic "ball-and-socket" interaction conserved at the B-type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two-residue "β-slip" type register shift in the β-strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered.


    Related Citations: 
    • Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
      Vedadi, M.,Lew, J.,Artz, J.,Amani, M.,Zhao, Y.,Dong, A.,Wasney, G.A.,Gao, M.,Hills, T.,Brokx, S.,Qiu, W.,Sharma, S.,Diassiti, A.,Alam, Z.,Melone, M.,Mulichak, A.,Wernimont, A.,Bray, J.,Loppnau, P.,Plotnikova, O.,Newberry, K.,Sundararajan, E.,Houston, S.,Walker, J.,Tempel, W.,Bochkarev, A.,Kozieradzki, I.,Edwards, A.,Arrowsmith, C.,Roos, D.,Kain, K.,Hui, R.
      (2007) Mol.Biochem.Parasitol. 151: 100


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, Oregon, 97239; Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon, 97331.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-Cys peroxiredoxin, putative
A, B, C, D, E, F, G, H, I, J
213Plasmodium vivax (strain Salvador I)Mutation(s): 0 
Find proteins for A5K421 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K421
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.550α = 90.00
b = 149.590β = 104.88
c = 131.910γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release