7KJ1

human peroxiredoxin 2 - C172S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • 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

Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2.

Peskin, A.V.Meotti, F.C.Kean, K.M.Gobl, C.Peixoto, A.S.Pace, P.E.Horne, C.R.Heath, S.G.Crowther, J.M.Dobson, R.C.J.Karplus, P.A.Winterbourn, C.C.

(2021) J Biol Chem 296: 100494-100494

  • DOI: 10.1016/j.jbc.2021.100494
  • Primary Citation of Related Structures:  
    7KIZ, 7KJ0, 7KJ1

  • PubMed Abstract: 
  • Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H 2 O 2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates, or undergoes hyperoxidation to the sulfinic acid ...

    Peroxiredoxin 2 (Prdx2) is a thiol peroxidase with an active site Cys (C52) that reacts rapidly with H 2 O 2 and other peroxides. The sulfenic acid product condenses with the resolving Cys (C172) to form a disulfide which is recycled by thioredoxin or GSH via mixed disulfide intermediates, or undergoes hyperoxidation to the sulfinic acid. C172 lies near the C-terminus, outside the active site. It is not established whether structural changes in this region, such as mixed disulfide formation, affect H 2 O 2 reactivity. To investigate, we designed mutants to cause minimal (C172S) or substantial (C172D and C172W) structural disruption. Stopped flow kinetics and mass spectrometry showed that mutation to Ser had minimal effect on rates of oxidation and hyperoxidation whereas Asp and Trp decreased both by ∼100-fold. To relate to structural changes, we solved the crystal structures of reduced wild-type and C172S Prdx2. The wild-type structure is highly similar to that of the published hyperoxidized form. C172S is closely related but more flexible and, as demonstrated by size exclusion chromatography and analytical ultracentrifugation, a weaker decamer. SEC and AUC showed that the C172D and C172W mutants are also weaker decamers than wild-type and small-angle X-ray scattering analysis indicated greater flexibility with partially unstructured regions consistent with C-terminal unfolding. We propose that these structural changes around C172 negatively impact the active site geometry to decrease reactivity with H 2 O 2 . This is relevant for Prdx turnover as intermediate mixed disulfides with C172 would also be disruptive, and could potentially react with peroxides before resolution is complete.


    Organizational Affiliation

    Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand. Electronic address: christine.winterbourn@otago.ac.nz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxiredoxin-2
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
197Homo sapiensMutation(s): 0 
Gene Names: PRDX2NKEFBTDPX1
EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for P32119 (Homo sapiens)
Explore P32119 
Go to UniProtKB:  P32119
PHAROS:  P32119
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.2α = 90
b = 88.3β = 99.2
c = 125.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM119227

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references