4RLE

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

• PDB DOI:  https://doi.org/10.2210/pdb4RLE/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-16 Released: 2014-12-03 
• Deposition Author(s): Dickmanns, A., Neumann, P., Ficner, R.

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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 

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

• PubMed: 25433025 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Molecular Structural Biology, and [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.67 kDa 
• Atom Count: 1,204 
• Modelled Residue Count: 116 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YaaQ	A	117	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU00290, yaaQ, darA
UniProt
Find proteins for P37538 (Bacillus subtilis (strain 168)) Explore P37538  Go to UniProtKB:  P37538

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA	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
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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 = 56.521	α = 90
b = 56.521	β = 90
c = 58.201	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Dickmanns, A., Neumann, P., Ficner, R.

Revision History  

• 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
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary