3TKQ | pdb_00003tkq

Crystal structure of full-length human peroxiredoxin 4 with mixed conformation

• PDB DOI: https://doi.org/10.2210/pdb3TKQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-28 Released: 2011-10-05 
• Deposition Author(s): Wang, X., Wang, L., Wang, X., Sun, F., Wang, C.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.224 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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 

• PubMed: 21916849 
• DOI: https://doi.org/10.1042/BJ20110380
• Primary Citation Related Structures: 
  3TKP, 3TKQ, 3TKR, 3TKS


• 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 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.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.06 kDa 
• Atom Count: 7,604 
• Modeled Residue Count: 873 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-4	A, B, C, D, E	246	Homo sapiens	Mutation(s): 0  Gene Names: PRDX4 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13162 (Homo sapiens) Explore Q13162  Go to UniProtKB:  Q13162
PHAROS:  Q13162 GTEx:  ENSG00000123131

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.224 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.486	α = 90
b = 139.518	β = 103.38
c = 96.197	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Wang, X., Wang, L., Wang, X., Sun, F., Wang, C.-C.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description