4UTO | pdb_00004uto

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

• PDB DOI: https://doi.org/10.2210/pdb4UTO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-07-22 Released: 2015-03-11 
• Deposition Author(s): Luo, Z., Counago, R.M., Maher, M., Kobe, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 

Starting Model: experimental

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

• PubMed: 25731976 
• DOI: https://doi.org/10.1038/ncomms7418
• Primary Citation 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. 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.
1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia [3] Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.
La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia.
1] School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia [2] School of Mathematics and Physics, University of Queensland, Brisbane, Queensland 4072, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.75 kDa 
• Atom Count: 4,976 
• Modeled Residue Count: 556 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN	A, B	309	Streptococcus pneumoniae	Mutation(s): 1
UniProt
Find proteins for P0A4G2 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P0A4G2  Go to UniProtKB:  P0A4G2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A], F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CD	C [auth A], E [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.737	α = 106.86
b = 59.292	β = 104.9
c = 62.468	γ = 93.37

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Luo, Z., Counago, R.M., Maher, M., Kobe, B.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 2.0: 2018-03-28
  Changes: Atomic model, Data collection, Database references, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description