4UTO

Crystal structure of pneumococcal surface antigen PsaA D280N in the Cd-bound, open state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Dysregulation of transition metal ion homeostasis is the molecular basis for cadmium toxicity in Streptococcus pneumoniae.

Begg, S.L., Eijkelkamp, B.A., Luo, Z., Counago, R.M., Morey, J.R., Maher, M.J., Ong, C.L., McEwan, A.G., Kobe, B., O'Mara, M.L., Paton, J.C., McDevitt, C.A.

(2015) Nat Commun 6: 6418-6418

  • DOI: 10.1038/ncomms7418
  • Primary Citation of Related Structures:  
    4UTO, 4UTP

  • PubMed Abstract: 

    • Cadmium is a transition metal ion that is highly toxic in biological systems. Although relatively rare in the Earth's crust, anthropogenic release of cadmium since industrialization has increased biogeochemical cycling and the abundance of the ion in the biosphere ...

    Cadmium is a transition metal ion that is highly toxic in biological systems. Although relatively rare in the Earth's crust, anthropogenic release of cadmium since industrialization has increased biogeochemical cycling and the abundance of the ion in the biosphere. Despite this, the molecular basis of its toxicity remains unclear. Here we combine metal-accumulation assays, high-resolution structural data and biochemical analyses to show that cadmium toxicity, in Streptococcus pneumoniae, occurs via perturbation of first row transition metal ion homeostasis. We show that cadmium uptake reduces the millimolar cellular accumulation of manganese and zinc, and thereby increases sensitivity to oxidative stress. Despite this, high cellular concentrations of cadmium (~17 mM) are tolerated, with negligible impact on growth or sensitivity to oxidative stress, when manganese and glutathione are abundant. Collectively, this work provides insight into the molecular basis of cadmium toxicity in prokaryotes, and the connection between cadmium accumulation and oxidative stress.

    Organizational Affiliation: 

    Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 4072, Australia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEINA, B309Streptococcus pneumoniaeMutation(s): 1 
Find proteins for P0A4G2 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P0A4G2 
Go to UniProtKB:  P0A4G2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS
Download Ideal Coordinates CCD File 
 D [auth A], F [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
CD
Query on CD
Download Ideal Coordinates CCD File 
 C [auth A], E [auth B]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.737α = 106.86
b = 59.292β = 104.9
c = 62.468γ = 93.37
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 2.0: 2018-03-28
    Changes: Atomic model, Data collection, Database references, Structure summary