3TKS

Crystal structure of full-length human peroxiredoxin 4 in three different redox states


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report



Literature

Structural insights into the peroxidase activity and inactivation of human peroxiredoxin 4

Wang, X.Wang, L.Wang, X.Sun, F.Wang, C.-C.

(2011) Biochem J 

  • DOI: 10.1042/BJ20110380
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Prx4 (peroxiredoxin 4) is the only peroxiredoxin located in the ER (endoplasmic reticulum) and a proposed scavenger for H2O2. In the present study, we solved crystal structures of human Prx4 in three different redox forms and characterized the reaction features of Prx4 with H2O2 ...

    Prx4 (peroxiredoxin 4) is the only peroxiredoxin located in the ER (endoplasmic reticulum) and a proposed scavenger for H2O2. In the present study, we solved crystal structures of human Prx4 in three different redox forms and characterized the reaction features of Prx4 with H2O2. Prx4 exhibits a toroid-shaped decamer constructed of five catalytic dimers. Structural analysis revealed conformational changes around helix α2 and the C-terminal reigon with a YF (Tyr-Phe) motif from the partner subunit, which are required for interchain disulfide formation between Cys87 and Cys208, a critical step of the catalysis. The structural explanation for the restricting role of the YF motif on the active site dynamics is provided in detail. Prx4 has a high reactivity with H2O2, but is susceptible to overoxidation and consequent inactivation by H2O2. Either deletion of the YF motif or dissociation into dimers decreased the susceptibility of Prx4 to overoxidation by increasing the flexibility of Cys87.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxiredoxin-4A, B246Homo sapiensMutation(s): 0 
Gene Names: PRDX4
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
Find proteins for Q13162 (Homo sapiens)
Explore Q13162 
Go to UniProtKB:  Q13162
NIH Common Fund Data Resources
PHAROS  Q13162
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxiredoxin-4C, D246Homo sapiensMutation(s): 0 
Gene Names: PRDX4
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
Find proteins for Q13162 (Homo sapiens)
Explore Q13162 
Go to UniProtKB:  Q13162
NIH Common Fund Data Resources
PHAROS  Q13162
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peroxiredoxin-4E246Homo sapiensMutation(s): 0 
Gene Names: PRDX4
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
Find proteins for Q13162 (Homo sapiens)
Explore Q13162 
Go to UniProtKB:  Q13162
NIH Common Fund Data Resources
PHAROS  Q13162
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PER
Query on PER

Download CCD File 
A, C, D
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
C,DL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.178α = 90
b = 140.104β = 102.48
c = 61.504γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release