5K2J

Crystal structure of reduced Prx3 in complex with h2o2 from Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of peroxiredoxin 3 fromVibrio vulnificusand its implications for scavenging peroxides and nitric oxide.

Ahn, J.Jang, K.K.Jo, I.Nurhasni, H.Lim, J.G.Yoo, J.W.Choi, S.H.Ha, N.C.

(2018) IUCrJ 5: 82-92

  • DOI: https://doi.org/10.1107/S205225251701750X
  • Primary Citation of Related Structures:  
    5K1G, 5K2I, 5K2J

  • PubMed Abstract: 

    Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidase enzymes. Recently, a new type of Prx, Vv Prx3, was identified in the pathogenic bacterium Vibrio vulnificus as being important for survival in macrophages. It employs only one catalytic cysteine residue to decompose peroxides. Here, crystal structures of Vv Prx3 representing its reduced and oxidized states have been determined, together with an H 2 O 2 -bound structure, at high resolution. The crystal structure representing the reduced Prx3 showed a typical dimeric interface, called the A-type interface. However, Vv Prx3 forms an oligomeric interface mediated by a disulfide bond between two catalytic cysteine residues from two adjacent dimers, which differs from the doughnut-like oligomers that appear in most Prxs. Subsequent biochemical studies showed that this disulfide bond was induced by treatment with nitric oxide (NO) as well as with peroxides. Consistently, NO treatment induced expression of the prx3 gene in V. vulnificus , and Vv Prx3 was crucial for the survival of bacteria in the presence of NO. Taken together, the function and mechanism of Vv Prx3 in scavenging peroxides and NO stress via oligomerization are proposed. These findings contribute to the understanding of the diverse functions of Prxs during pathogenic processes at the molecular level.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-Cys peroxiredoxin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
164Vibrio vulnificus MO6-24/OMutation(s): 0 
UniProt
Find proteins for A0A1Z0YU25 (Vibrio vulnificus (strain MO6-24/O))
Explore A0A1Z0YU25 
Go to UniProtKB:  A0A1Z0YU25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z0YU25
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.08α = 78.72
b = 97.725β = 67.33
c = 97.492γ = 67.34
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description