7R2Y

Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with ATP resulting from short ATP soak, conflicting T-loop and C-loop with partial occupancy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Carbon signaling protein SbtB possesses atypical redox-regulated apyrase activity to facilitate regulation of bicarbonate transporter SbtA.

Selim, K.A.Haffner, M.Mantovani, O.Albrecht, R.Zhu, H.Hagemann, M.Forchhammer, K.Hartmann, M.D.

(2023) Proc Natl Acad Sci U S A 120: e2205882120-e2205882120

  • DOI: https://doi.org/10.1073/pnas.2205882120
  • Primary Citation of Related Structures:  
    7R2Y, 7R2Z, 7R30, 7R31, 7R32

  • PubMed Abstract: 

    The PII superfamily consists of widespread signal transduction proteins found in all domains of life. In addition to canonical PII proteins involved in C/N sensing, structurally similar PII-like proteins evolved to fulfill diverse, yet poorly understood cellular functions. In cyanobacteria, the bicarbonate transporter SbtA is co-transcribed with the conserved PII-like protein, SbtB, to augment intracellular inorganic carbon levels for efficient CO 2 fixation. We identified SbtB as a sensor of various adenine nucleotides including the second messenger nucleotides cyclic AMP (cAMP) and c-di-AMP. Moreover, many SbtB proteins possess a C-terminal extension with a disulfide bridge of potential redox-regulatory function, which we call R-loop. Here, we reveal an unusual ATP/ADP apyrase (diphosphohydrolase) activity of SbtB that is controlled by the R-loop. We followed the sequence of hydrolysis reactions from ATP over ADP to AMP in crystallographic snapshots and unravel the structural mechanism by which changes of the R-loop redox state modulate apyrase activity. We further gathered evidence that this redox state is controlled by thioredoxin, suggesting that it is generally linked to cellular metabolism, which is supported by physiological alterations in site-specific mutants of the SbtB protein. Finally, we present a refined model of how SbtB regulates SbtA activity, in which both the apyrase activity and its redox regulation play a central role. This highlights SbtB as a central switch point in cyanobacterial cell physiology, integrating not only signals from the energy state (adenyl-nucleotide binding) and the carbon supply via cAMP binding but also from the day/night status reported by the C-terminal redox switch.


  • Organizational Affiliation

    Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.833α = 90
b = 63.833β = 90
c = 81.231γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description