4FH8 | pdb_00004fh8

Crystal Structure of Peroxiredoxin-1 from the human hookworm Ancylostoma ceylanicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.214 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Peroxiredoxin-1 from the Human Hookworm Ancylostoma ceylanicum Forms a Stable Oxidized Decamer and Is Covalently Inhibited by Conoidin A.

Nguyen, J.B.Pool, C.D.Wong, C.Y.Treger, R.S.Williams, D.L.Cappello, M.Lea, W.A.Simeonov, A.Vermeire, J.J.Modis, Y.

(2013) Chem Biol 20: 991-1001

  • DOI: https://doi.org/10.1016/j.chembiol.2013.06.011
  • Primary Citation Related Structures: 
    4FH8, 4KW6

  • PubMed Abstract: 

    Hookworms are parasitic nematodes that have a devastating impact on global health, particularly in developing countries. We report a biochemical and structural analysis of a peroxiredoxin from the hookworm Ancylostoma ceylanicum, AcePrx-1. Peroxiredoxins provide antioxidant protection and act as signaling molecules and chaperones. AcePrx-1 is expressed in adult hookworms and can be inactivated by 2,3-bis(bromomethyl)quinoxaline-1,4-dioxide (conoidin A). Conoidin A inactivates AcePrx-1 by alkylating or crosslinking the catalytic cysteines, while maintaining the enzyme in the "locally unfolded" conformation. Irreversible oxidation of the resolving cysteine may contribute additional inhibitory activity. A crystal structure of oxidized AcePrx-1 reveals a disulfide-linked decamer. A helix macrodipole near the active site increases the reactivity of the catalytic cysteines to conoidin A. This work demonstrates the promise of conoidin compounds as probes to evaluate peroxiredoxins as drug targets in human parasites.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecule Content 

  • Total Structure Weight: 229.98 kDa 
  • Atom Count: 14,009 
  • Modeled Residue Count: 1,694 
  • Deposited Residue Count: 2,040 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AcePrx-1
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
204Ancylostoma ceylanicumMutation(s): 0 
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for J7HJM3 (Ancylostoma ceylanicum)
Explore J7HJM3 
Go to UniProtKB:  J7HJM3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7HJM3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.214 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.688α = 90
b = 146.282β = 95.24
c = 136.03γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2013-09-11
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary