4WK1

Crystal structure of Staphylococcus aureus PstA in complex with c-di-AMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 

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


Literature

c-di-AMP recognition by Staphylococcus aureus PstA.

Muller, M., Hopfner, K., Witte, G.

(2015) FEBS Lett 589: 45-51

  • DOI: https://doi.org/10.1016/j.febslet.2014.11.022
  • Primary Citation of Related Structures:  
    4WK1, 4WK3

  • PubMed Abstract: 

    Cyclic-di-AMP (c-di-AMP) is a bacterial secondary messenger involved in various processes, including sensing of DNA-integrity, cell wall metabolism and potassium transport. A number of c-di-AMP receptor proteins have recently been identified in Staphylococcus aureus. One of them - PstA - possesses a ferredoxin-like fold and is structurally related to the class of PII signal-transduction proteins. PII proteins are involved in a large number of pathways, most of them associated with nitrogen metabolism. In this study we describe the mode of c-di-AMP binding and subsequent structural changes of S. aureus PstA. An altered architecture in PstA compared to canonical PII proteins results in differences in ligand coordination.

    • Organizational Affiliation: 

    Ludwig-Maximilians-Universität München, Gene Center and Dept. of Biochemistry, Feodor-Lynen-Str. 25, 81377 Munich, Germany.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PstA129Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: SACOL0525
UniProt
Find proteins for A0A0H2WXZ7 (Staphylococcus aureus (strain COL))
Explore A0A0H2WXZ7 
Go to UniProtKB:  A0A0H2WXZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WXZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2BA
Query on 2BA
Download Ideal Coordinates CCD File 
B [auth A](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
C20 H24 N10 O12 P2
PDXMFTWFFKBFIN-XPWFQUROSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2BA Binding MOAD:  4WK1 Kd: 109 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.1α = 90
b = 68.1β = 90
c = 135.74γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermany3717/2-1
German Research FoundationGermanyGRK1721

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2014-12-31
    Changes: Database references
  • Version 2.0: 2024-01-10
    Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary