1OC3

HUMAN PEROXIREDOXIN 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Dimeric Oxidized Form of Human Peroxiredoxin 5

Evrard, C.Capron, A.Marchand, C.Clippe, A.Wattiez, R.Soumillion, P.Knoops, B.Declercq, J.-P.

(2004) J.Mol.Biol. 337: 1079

  • DOI: 10.1016/j.jmb.2004.02.017

  • PubMed Abstract: 
  • Peroxiredoxin 5 is the last discovered mammalian member of an ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Mammalian peroxiredoxin 5 has been recently classified as an atypical 2-Cys peroxiredoxin due to the p ...

    Peroxiredoxin 5 is the last discovered mammalian member of an ubiquitous family of peroxidases widely distributed among prokaryotes and eukaryotes. Mammalian peroxiredoxin 5 has been recently classified as an atypical 2-Cys peroxiredoxin due to the presence of a conserved peroxidatic N-terminal cysteine (Cys47) and an unconserved resolving C-terminal cysteine residue (Cys151) forming an intramolecular disulfide intermediate in the oxidized enzyme. We have recently reported the crystal structure of human peroxiredoxin 5 in its reduced form. Here, a new crystal form of human peroxiredoxin 5 is described at 2.0 A resolution. The asymmetric unit contains three polypeptide chains. Surprisingly, beside two reduced chains, the third one is oxidized although the enzyme was crystallized under initial reducing conditions in the presence of 1 mM 1,4-dithio-dl-threitol. The oxidized polypeptide chain forms an homodimer with a symmetry-related one through intermolecular disulfide bonds between Cys47 and Cys151. The formation of these disulfide bonds is accompanied by the partial unwinding of the N-terminal parts of the alpha2 helix, which, in the reduced form, contains the peroxidatic Cys47 and the alpha6 helix, which is sequentially close to the resolving residue Cys151. In each monomer of the oxidized chain, the C-terminal part including the alpha6 helix is completely reorganized and is isolated from the rest of the protein on an extended arm. In the oxidized dimer, the arm belonging to the first monomer now appears at the surface of the second subunit and vice versa.


    Related Citations: 
    • Cloning and Characterization of Aoeb166, a Novel Mammalian Antioxidant Enzyme of the Peroxiredoxin Family
      Knoops, B.,Clippe, A.,Bogard, C.,Arsalane, K.,Wattiez, R.,Hermans, C.,Duconseille, E.,Falmagne, P.,Bernard, A.
      (1999) J.Biol.Chem. 274: 30451
    • A Twinned Monoclinic Crystal Form of Human Peroxiredoxin 5 with Eight Molecules in the Asymmetric Unit
      Declercq, J.P.,Evrard, C.
      (2001) Acta Crystallogr.,Sect.D D57: 1829
    • Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution
      Declercq, J.P.,Evrard, C.,Clippe, A.,Stricht, D.V.,Bernard, A.,Knoops, B.
      (2001) J.Mol.Biol. 311: 751


    Organizational Affiliation

    Unit of Structural Chemistry (CSTR), Université catholique de Louvain, 1 place Louis Pasteur, B-1348 Louvain-la-Neuve, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXIREDOXIN 5
A, B, C
172Homo sapiensMutation(s): 0 
Gene Names: PRDX5 (ACR1)
EC: 1.11.1.15
Find proteins for P30044 (Homo sapiens)
Go to Gene View: PRDX5
Go to UniProtKB:  P30044
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.195α = 90.00
b = 102.053β = 90.00
c = 145.060γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-10-24
    Type: Data collection, Source and taxonomy