2Z9S

Crystal Structure Analysis of rat HBP23/Peroxiredoxin I, Cys52Ser mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dimer-Oligomer Interconversion of Wild-type and Mutant Rat 2-Cys Peroxiredoxin: DISULFIDE FORMATION AT DIMER-DIMER INTERFACES IS NOT ESSENTIAL FOR DECAMERIZATION

Matsumura, T.Okamoto, K.Iwahara, S.Hori, H.Takahashi, Y.Nishino, T.Abe, Y.

(2008) J.Biol.Chem. 283: 284-293

  • DOI: 10.1074/jbc.M705753200

  • PubMed Abstract: 
  • Rat heme-binding protein 23 (HBP23)/peroxiredoxin (Prx I) belongs to the 2-Cys peroxiredoxin type I family and exhibits peroxidase activity coupled with reduced thioredoxin (Trx) as an electron donor. We analyzed the dimer-oligomer interconversion of ...

    Rat heme-binding protein 23 (HBP23)/peroxiredoxin (Prx I) belongs to the 2-Cys peroxiredoxin type I family and exhibits peroxidase activity coupled with reduced thioredoxin (Trx) as an electron donor. We analyzed the dimer-oligomer interconversion of wild-type and mutant HBP23/Prx I by gel filtration and found that the C52S and C173S mutants existed mostly as decamers, whereas the wild type was a mixture of various forms, favoring the decamer at higher protein concentration and lower ionic salt concentration and in the presence of dithiothreitol. The C83S mutant was predominantly dimeric, in agreement with a previous crystallographic analysis (Hirotsu, S., Abe, Y., Okada, K., Nagahara, N., Hori, H., Nishino, T., and Hakoshima, T. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 12333-12338). X-ray diffraction analysis of the decameric C52S mutant revealed a toroidal structure (diameter, approximately 130A; inside diameter, approximately 55A; thickness, approximately 45A). In contrast to human Prx I, which was recently reported to exist predominantly as the decamer with Cys(83)-Cys(83) disulfide bonds at all dimer-dimer interfaces, rat HBP23/Prx I has a Cys(83)-Cys(83) disulfide bond at only one dimer-dimer interface (S-S separation of approximately 2.1A), whereas the interactions at the other interfaces (mean S-S separation of 3.6A) appear to involve hydrophobic and van der Waals forces. This finding is consistent with gel filtration analyses showing that the protein readily interconverts between dimer and oligomeric forms. The C83S mutant exhibited similar peroxidase activity to the wild type, which is exclusively dimeric, in the Trx/Trx reductase system. At higher concentrations, where the protein was mostly decameric, less efficient attack of reduced Trx was observed in a [(14)C]iodoacetamide incorporation experiment. We suggest that the dimerdecamer interconversion may have a regulatory role.


    Related Citations: 
    • Crystal structure of a multifunctional 2-Cys peroxiredoxin heme-binding protein 23 kDa/proliferation-associated gene product
      Hirotsu, S.,Abe, Y.,Okada, K.,Nagahara, N.,Hori, H.,Nishino, T.,Hakoshima, T.
      (1999) Proc.Natl.Acad.Sci.Usa 96: 12333


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxiredoxin-1
A, B, C, D, E, F, G, H, I, J
199Rattus norvegicusMutation(s): 1 
Gene Names: Prdx1 (Tdpx2)
EC: 1.11.1.15
Find proteins for Q63716 (Rattus norvegicus)
Go to UniProtKB:  Q63716
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.312α = 90.00
b = 111.637β = 112.03
c = 120.740γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
ADSCdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance