4D3H

Structure of PstA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Complex Structure and Biochemical Characterization of the Staphylococcus Aureus Cyclic Di-AMP Binding Protein Psta, the Founding Member of a New Signal Transduction Protein Family

Campeotto, I.Zhang, Y.Mladenov, M.G.Freemont, P.S.Grundling, A.

(2015) J.Biol.Chem. 290: 2888

  • DOI: 10.1074/jbc.M114.621789
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Signaling nucleotides are integral parts of signal transduction systems allowing bacteria to cope with and rapidly respond to changes in the environment. The Staphylococcus aureus PII-like signal transduction protein PstA was recently identified as a ...

    Signaling nucleotides are integral parts of signal transduction systems allowing bacteria to cope with and rapidly respond to changes in the environment. The Staphylococcus aureus PII-like signal transduction protein PstA was recently identified as a cyclic diadenylate monophosphate (c-di-AMP)-binding protein. Here, we present the crystal structures of the apo- and c-di-AMP-bound PstA protein, which is trimeric in solution as well as in the crystals. The structures combined with detailed bioinformatics analysis revealed that the protein belongs to a new family of proteins with a similar core fold but with distinct features to classical PII proteins, which usually function in nitrogen metabolism pathways in bacteria. The complex structure revealed three identical c-di-AMP-binding sites per trimer with each binding site at a monomer-monomer interface. Although distinctly different from other cyclic-di-nucleotide-binding sites, as the half-binding sites are not symmetrical, the complex structure also highlighted common features for c-di-AMP-binding sites. A comparison between the apo and complex structures revealed a series of conformational changes that result in the ordering of two anti-parallel β-strands that protrude from each monomer and allowed us to propose a mechanism on how the PstA protein functions as a signaling transduction protein.


    Organizational Affiliation

    From the Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PSTA
A, B, C
128Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Find proteins for Q2G229 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G229
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BA
Query on 2BA

Download SDF File 
Download CCD File 
A, B, C
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
C20 H24 N10 O12 P2
PDXMFTWFFKBFIN-XPWFQUROSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2BAKd: 370 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.206α = 90.00
b = 65.655β = 95.98
c = 85.156γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2014-12-31
    Type: Database references
  • Version 1.2: 2015-02-11
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Data collection