Crystal Structure of L. monocytogenes PstA in complex with cyclic-di-AMP

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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Molecular basis for the recognition of cyclic-di-AMP by PstA, a PII -like signal transduction protein.

Choi, P.H.Sureka, K.Woodward, J.J.Tong, L.

(2015) Microbiologyopen 4: 361-374

  • DOI: https://doi.org/10.1002/mbo3.243
  • Primary Citation of Related Structures:  
    4RWW, 4RWX

  • PubMed Abstract: 

    Cyclic-di-AMP (c-di-AMP) is a broadly conserved bacterial second messenger that is of importance in bacterial physiology. The molecular receptors mediating the cellular responses to the c-di-AMP signal are just beginning to be discovered. PstA is a previously uncharacterized PII -like protein which has been identified as a c-di-AMP receptor. PstA is widely distributed and conserved among Gram-positive bacteria in the phylum Firmicutes. Here, we report the biochemical, structural, and functional characterization of PstA from Listeria monocytogenes. We have determined the crystal structures of PstA in the c-di-AMP-bound and apo forms at 1.6 and 2.9 Å resolution, respectively, which provide the molecular basis for its specific recognition of c-di-AMP. PstA forms a homotrimer structure that has overall similarity to the PII protein family which binds ATP. However, PstA is markedly different from PII proteins in the loop regions, and these structural differences mediate the specific recognition of their respective nucleotide ligand. The residues composing the c-di-AMP binding pocket are conserved, suggesting that c-di-AMP recognition by PstA is of functional importance. Disruption of pstA in L. monocytogenes affected c-di-AMP-mediated alterations in bacterial growth and lysis. Overall, we have defined the PstA family as a conserved and specific c-di-AMP receptor in bacteria.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York City, New York, 10027.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lmo2692 protein
A, B, C
113Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: lmo2692
Find proteins for Q8Y3Y7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y3Y7 
Go to UniProtKB:  Q8Y3Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y3Y7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2BA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth B],
G [auth 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
C20 H24 N10 O12 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.108α = 110.8
b = 51.788β = 105.59
c = 52.996γ = 109.84
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-03-13
    Changes: Source and taxonomy