7BVV

Crystal structure of sulfonic peroxiredoxin Ahp1 in complex with thioredoxin Trx2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of sulfonic peroxiredoxin Ahp1 in complex with thioredoxin Trx2 mimics a conformational intermediate during the catalytic cycle.

Lian, F.M.Jiang, Y.L.Yang, W.Yang, X.

(2020) Int J Biol Macromol 161: 1055-1060

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.06.065
  • Primary Citation of Related Structures:  
    7BVV

  • PubMed Abstract: 

    Peroxiredoxin (Prx) is a thiol-based peroxidase that eliminates reactive oxygen species to avoid oxidative damage. Alkyl hydroperoxide reductase Ahp1 is a novel and specific typical 2-cysteine Prx. Here, we present the crystal structure of sulfonic Ahp1 complexed with thioredoxin Trx2 at 2.12 Å resolution. This structure implies that the transient Ahp1-Trx2 complex during the catalytic cycle already have an ability to decompose the peroxides. Structural analysis reveals that the segment glutamine23-lysine32 juxtaposed to the resolving cysteine (C R ) of Ahp1 moves inward to generate a compact structure upon peroxidatic cysteine (C P ) overoxidation, resulting in the breakdown of several conserved hydrogen bonds formed by Ahp1-Trx2 complex interaction. Structural comparisons suggest that the structure of sulfonic Ahp1 represents a novel conformation of Ahp1, which can mimic a conformational intermediate between the reduced and oxidized forms. Therefore, this study may provide a new structural insight into the intermediate state in which the segment glutamine23-lysine32 juxtaposed to the cysteine31 (C R ) undergoes a conformational change upon cysteine62 (C P ) oxidation to prepare for the formation of an intermolecular C P -C R disulfide bond during Ahp1 catalytic cycle.


  • Organizational Affiliation

    Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong 272067, People's Republic of China; Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China. Electronic address: fmlian@mail.jnmc.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin AHP1176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AHP1YLR109WL2916L9354.5
EC: 1.11.1.15
UniProt
Find proteins for P38013 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38013 
Go to UniProtKB:  P38013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38013
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-2112Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: TRX2TRX1YGR209CG7746
UniProt
Find proteins for P22803 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22803 
Go to UniProtKB:  P22803
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22803
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.5α = 90
b = 132.8β = 90
c = 76.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description