4RLE

Crystal structure of the c-di-AMP binding PII-like protein DarA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

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This is version 1.3 of the entry. See complete history


Literature

Identification, Characterization, and Structure Analysis of the Cyclic di-AMP-binding PII-like Signal Transduction Protein DarA.

Gundlach, J.Dickmanns, A.Schroder-Tittmann, K.Neumann, P.Kaesler, J.Kampf, J.Herzberg, C.Hammer, E.Schwede, F.Kaever, V.Tittmann, K.Stulke, J.Ficner, R.

(2015) J Biol Chem 290: 3069-3080

  • DOI: 10.1074/jbc.M114.619619
  • Primary Citation of Related Structures:  
    4RLE

  • PubMed Abstract: 
  • The cyclic dimeric AMP nucleotide c-di-AMP is an essential second messenger in Bacillus subtilis. We have identified the protein DarA as one of the prominent c-di-AMP receptors in B. subtilis. Crystal structure analysis shows that DarA is highly homologous to PII signal transducer proteins ...

    The cyclic dimeric AMP nucleotide c-di-AMP is an essential second messenger in Bacillus subtilis. We have identified the protein DarA as one of the prominent c-di-AMP receptors in B. subtilis. Crystal structure analysis shows that DarA is highly homologous to PII signal transducer proteins. In contrast to PII proteins, the functionally important B- and T-loops are swapped with respect to their size. DarA is a homotrimer that binds three molecules of c-di-AMP, each in a pocket located between two subunits. We demonstrate that DarA is capable to bind c-di-AMP and with lower affinity cyclic GMP-AMP (3'3'-cGAMP) but not c-di-GMP or 2'3'-cGAMP. Consistently the crystal structure shows that within the ligand-binding pocket only one adenine is highly specifically recognized, whereas the pocket for the other adenine appears to be promiscuous. Comparison with a homologous ligand-free DarA structure reveals that c-di-AMP binding is accompanied by conformational changes of both the fold and the position of the B-loop in DarA.


    Organizational Affiliation

    Molecular Structural Biology, and rficner@uni-goettingen.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YaaQA117Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU00290yaaQdarA
UniProt
Find proteins for P37538 (Bacillus subtilis (strain 168))
Explore P37538 
Go to UniProtKB:  P37538
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37538
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.521α = 90
b = 56.521β = 90
c = 58.201γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2015-02-11
    Changes: Database references
  • Version 1.3: 2019-09-04
    Changes: Data collection