7OBJ

Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with cyclic di-AMP (c-di-AMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Diurnal metabolic control in cyanobacteria requires perception of second messenger signaling molecule c-di-AMP by the carbon control protein SbtB.

Selim, K.A.Haffner, M.Burkhardt, M.Mantovani, O.Neumann, N.Albrecht, R.Seifert, R.Kruger, L.Stulke, J.Hartmann, M.D.Hagemann, M.Forchhammer, K.

(2021) Sci Adv 7: eabk0568-eabk0568

  • DOI: https://doi.org/10.1126/sciadv.abk0568
  • Primary Citation of Related Structures:  
    7OBJ

  • PubMed Abstract: 

    Because of their photosynthesis-dependent lifestyle, cyanobacteria evolved sophisticated regulatory mechanisms to adapt to oscillating day-night metabolic changes. How they coordinate the metabolic switch between autotrophic and glycogen-catabolic metabolism in light and darkness is poorly understood. Recently, c-di-AMP has been implicated in diurnal regulation, but its mode of action remains elusive. To unravel the signaling functions of c-di-AMP in cyanobacteria, we isolated c-di-AMP receptor proteins. Thereby, the carbon-sensor protein SbtB was identified as a major c-di-AMP receptor, which we confirmed biochemically and by x-ray crystallography. In search for the c-di-AMP signaling function of SbtB, we found that both SbtB and c-di-AMP cyclase–deficient mutants showed reduced diurnal growth and that c-di-AMP–bound SbtB interacts specifically with the glycogen-branching enzyme GlgB. Accordingly, both mutants displayed impaired glycogen synthesis during the day and impaired nighttime survival. Thus, the pivotal role of c-di-AMP in day-night acclimation can be attributed to SbtB-mediated regulation of glycogen metabolism.


  • Organizational Affiliation

    Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Auf der Morgenstelle 28, 72076 Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-associated protein slr1513
A, B, C
120Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: slr1513
UniProt
Find proteins for P73954 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73954 
Go to UniProtKB:  P73954
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73954
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2BA (Subject of Investigation/LOI)
Query on 2BA

Download Ideal Coordinates CCD File 
D [auth A],
E [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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.171α = 90
b = 63.171β = 90
c = 81.733γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description