5KS7

Crystal structure of Listeria monocytogenes OpuCA CBS domain dimer in complex with cyclic-di-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Cyclic di-AMP targets the cystathionine beta-synthase domain of the osmolyte transporter OpuC.

Huynh, T.N.Choi, P.H.Sureka, K.Ledvina, H.E.Campillo, J.Tong, L.Woodward, J.J.

(2016) Mol Microbiol 102: 233-243

  • DOI: https://doi.org/10.1111/mmi.13456
  • Primary Citation of Related Structures:  
    5KS7

  • PubMed Abstract: 

    Cellular turgor is of fundamental importance to bacterial growth and survival. Changes in external osmolarity as a consequence of fluctuating environmental conditions and colonization of diverse environments can significantly impact cytoplasmic water content, resulting in cellular lysis or plasmolysis. To ensure maintenance of appropriate cellular turgor, bacteria import ions and small organic osmolytes, deemed compatible solutes, to equilibrate cytoplasmic osmolarity with the extracellular environment. Here, we show that elevated levels of c-di-AMP, a ubiquitous second messenger among bacteria, result in significant susceptibility to elevated osmotic stress in the bacterial pathogen Listeria monocytogenes. We found that levels of import of the compatible solute carnitine show an inverse correlation with intracellular c-di-AMP content and that c-di-AMP directly binds to the CBS domain of the ATPase subunit of the carnitine importer OpuC. Biochemical and structural studies identify conserved residues required for this interaction and transport activity in bacterial cells. Overall, these studies reveal a role for c-di-AMP mediated regulation of compatible solute import and provide new insight into the molecular mechanisms by which this essential second messenger impacts bacterial physiology and adaptation to changing environmental conditions.


  • Organizational Affiliation

    Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carnitine transport ATP-binding protein OpuCA
A, B
126Listeria monocytogenesMutation(s): 0 
Gene Names: opuCA
EC: 3.6.3.32 (PDB Primary Data), 7.6.2.9 (UniProt)
UniProt
Find proteins for Q9KHT9 (Listeria monocytogenes)
Explore Q9KHT9 
Go to UniProtKB:  Q9KHT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KHT9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2BA
Query on 2BA

Download Ideal Coordinates CCD File 
C [auth B](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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.342α = 90
b = 43.861β = 94.94
c = 68.841γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI116669
National Institutes of Health/Office of the DirectorUnited StatesOD012018

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description