4NUK

Crystal structure of nickel-bound Na-ASP-2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Probing the equatorial groove of the hookworm protein and vaccine candidate antigen, Na-ASP-2.

Mason, L., Tribolet, L., Simon, A., von Gnielinski, N., Nienaber, L., Taylor, P., Willis, C., Jones, M.K., Sternberg, P.W., Gasser, R.B., Loukas, A., Hofmann, A.

(2014) Int.J.Biochem.Cell Biol. 50: 146-155

  • DOI: 10.1016/j.biocel.2014.03.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Hookworm activation-associated secreted proteins can be structurally classified into at least three different groups. The hallmark feature of Group 1 activation-associated secreted proteins is a prominent equatorial groove, which is inferred to form ...

    Hookworm activation-associated secreted proteins can be structurally classified into at least three different groups. The hallmark feature of Group 1 activation-associated secreted proteins is a prominent equatorial groove, which is inferred to form a ligand binding site. Furthermore, a conserved tandem histidine motif is located in the centre of the groove and believed to provide or support a yet to be determined catalytic activity. Here, we report three-dimensional crystal structures of Na-ASP-2, an L3-secreted activation-associated secreted protein from the human hookworm Necator americanus, which demonstrate transition metal binding ability of the conserved tandem histidine motif. We further identified moderate phosphohydrolase activity of recombinant Na-ASP-2, which relates to the tandem histidine motif. By panning a random 12-mer peptide phage library, we identified a peptide with high similarity to the human calcium-activated potassium channel SK3, and confirm binding of the synthetic peptide to recombinant Na-ASP-2 by differential scanning fluorimetry. Potential binding modes of the peptide to Na-ASP-2 were studied by molecular dynamics simulations which clearly identify a preferred topology of the Na-ASP-2:SK3 peptide complex.

    Organizational Affiliation: 

    Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ancylostoma secreted protein 2
A
210Necator americanusGene Names: ASP2
Find proteins for J9ULM6 (Necator americanus)
Go to UniProtKB:  J9ULM6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI
Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.921α = 90.00
b = 61.958β = 90.00
c = 77.082γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
ADSCdata collection
PHASERphasing
PHENIXmodel building
XDSdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


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Entry History 

Deposition Data

  • Deposited Date: 2013-12-03 
  • Released Date: 2014-05-14 
  • Deposition Author(s): Hofmann, A.

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release