3ZK8

CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA E205Q IN THE METAL-FREE, OPEN STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Imperfect coordination chemistry facilitates metal ion release in the Psa permease.

Counago, R.M.Ween, M.P.Begg, S.L.Bajaj, M.Zuegg, J.O'Mara, M.L.Cooper, M.A.McEwan, A.G.Paton, J.C.Kobe, B.McDevitt, C.A.

(2014) Nat Chem Biol 10: 35-41

  • DOI: https://doi.org/10.1038/nchembio.1382
  • Primary Citation of Related Structures:  
    3ZK7, 3ZK8, 3ZK9, 3ZKA

  • PubMed Abstract: 

    The relative stability of divalent first-row transition metal ion complexes, as defined by the Irving-Williams series, poses a fundamental chemical challenge for selectivity in bacterial metal ion acquisition. Here we show that although the substrate-binding protein of Streptococcus pneumoniae, PsaA, is finely attuned to bind its physiological substrate manganese, it can also bind a broad range of other divalent transition metal cations. By combining high-resolution structural data, metal-binding assays and mutational analyses, we show that the inability of open-state PsaA to satisfy the preferred coordination chemistry of manganese enables the protein to undergo the conformational changes required for cargo release to the Psa permease. This is specific for manganese ions, whereas zinc ions remain bound to PsaA. Collectively, these findings suggest a new ligand binding and release mechanism for PsaA and related substrate-binding proteins that facilitate specificity for divalent cations during competition from zinc ions, which are more abundant in biological systems.


  • Organizational Affiliation

    1] School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia. [2] Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia. [3].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
A, B
278Streptococcus pneumoniaeMutation(s): 1 
UniProt
Find proteins for P0A4G2 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P0A4G2 
Go to UniProtKB:  P0A4G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A4G2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.77α = 106.4
b = 59.07β = 105.05
c = 62.21γ = 93.55
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2014-01-08
    Changes: Database references
  • Version 2.0: 2018-03-28
    Changes: Atomic model, Data collection, Database references, Structure summary
  • Version 2.1: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description