4RLE | pdb_00004rle

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 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

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 Biological Chem 290: 3069-3080

• PubMed: 25433025 
• DOI: https://doi.org/10.1074/jbc.M114.619619
• Primary Citation 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: 
• From the Departments of General Microbiology.
Molecular Structural Biology, and.
Molecular Enzymology, Georg August University Göttingen, 37077 Göttingen, Germany.
Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
BIOLOG Life Science Institute, 28199 Bremen, Germany, and.
Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany.
From the Departments of General Microbiology, [e-mail].
Molecular Structural Biology, and [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
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 
• Modeled 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
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 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

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