6ZZA | pdb_00006zza

Crystal structure of CbpB in complex with c-di-AMP

• PDB DOI: https://doi.org/10.2210/pdb6ZZA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Streptococcus agalactiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-04 Released: 2021-08-18 
• Deposition Author(s): Mechaly, A.E., Covaleda-Cortes, G., Kaminski, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.245 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

The c-di-AMP-binding protein CbpB modulates the level of ppGpp alarmone in Streptococcus agalactiae.

Covaleda-Cortes, G., Mechaly, A., Brissac, T., Baehre, H., Devaux, L., England, P., Raynal, B., Hoos, S., Gominet, M., Firon, A., Trieu-Cuot, P., Kaminski, P.A.

(2023) FEBS J 290: 2968-2992

• PubMed: 36629470 
• DOI: https://doi.org/10.1111/febs.16724
• Primary Citation Related Structures: 
  6ZZ9, 6ZZA


• PubMed Abstract: 
  

  Cyclic di-AMP is an essential signalling molecule in Gram-positive bacteria. This second messenger regulates the osmotic pressure of the cell by interacting directly with the regulatory domains, either RCK_C or CBS domains, of several potassium and osmolyte uptake membrane protein systems. Cyclic di-AMP also targets stand-alone CBS domain proteins such as DarB in Bacillus subtilis and CbpB in Listeria monocytogenes. We show here that the CbpB protein of Group B Streptococcus binds c-di-AMP with a very high affinity. Crystal structures of CbpB reveal the determinants of binding specificity and significant conformational changes occurring upon c-di-AMP binding. Deletion of the cbpB gene alters bacterial growth in low potassium conditions most likely due to a decrease in the amount of ppGpp caused by a loss of interaction between CbpB and Rel, the GTP/GDP pyrophosphokinase.

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Organizational Affiliation: 
• Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France.
CNRS-UMR 3528, Crystallography Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France.
Research Core Unit Metabolomics, Hannover Medical School, Germany.
CNRS UMR 3528, Molecular Biophysics Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.6 kDa 
• Atom Count: 1,288 
• Modeled Residue Count: 150 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBS domain-containing protein	A	176	Streptococcus agalactiae	Mutation(s): 0  Gene Names: ykuL, C6N06_01440, D5F95_08070, DX05_08405, E8E04_03435, F5F86_02645, NCTC9828_00932, WA02_02795, WA05_04310
UniProt
Find proteins for A0A076YWK5 (Streptococcus agalactiae) Explore A0A076YWK5  Go to UniProtKB:  A0A076YWK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BA (Subject of Investigation/LOI)	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
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.245 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.83	α = 90
b = 93.83	β = 90
c = 33.6	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Mechaly, A.E., Covaleda-Cortes, G., Kaminski, P.A.

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2025-08-13
  Changes: Database references, Structure summary