6ZZ9

Crystal structure of CbpB from Streptococcus agalactiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 

  • DOI: https://doi.org/10.1111/febs.16724
  • Primary Citation of Related Structures:  
    6ZZ9

  • 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.


  • Organizational Affiliation

    Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CBS domain-containing protein
A, B
176Streptococcus agalactiaeMutation(s): 0 
Gene Names: ykuLC6N06_01440D5F95_08070DX05_08405E8E04_03435F5F86_02645NCTC9828_00932WA02_02795WA05_04310
UniProt
Find proteins for A0A076YWK5 (Streptococcus agalactiae)
Explore A0A076YWK5 
Go to UniProtKB:  A0A076YWK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A076YWK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.61α = 90
b = 60.61β = 90
c = 190.47γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
AutoSolphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references