5O3Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

PII-like signaling protein SbtB links cAMP sensing with cyanobacterial inorganic carbon response.

Selim, K.A.Haase, F.Hartmann, M.D.Hagemann, M.Forchhammer, K.

(2018) Proc Natl Acad Sci U S A 115: E4861-E4869

  • DOI: https://doi.org/10.1073/pnas.1803790115
  • Primary Citation of Related Structures:  
    5O3P, 5O3Q, 5O3R, 5O3S

  • PubMed Abstract: 

    Cyanobacteria are phototrophic prokaryotes that evolved oxygenic photosynthesis ∼2.7 billion y ago and are presently responsible for ∼10% of total global photosynthetic production. To cope with the evolutionary pressure of dropping ambient CO 2 concentrations, they evolved a CO 2 -concentrating mechanism (CCM) to augment intracellular inorganic carbon (C i ) levels for efficient CO 2 fixation. However, how cyanobacteria sense the fluctuation in C i is poorly understood. Here we present biochemical, structural, and physiological insights into SbtB, a unique P II -like signaling protein, which provides new insights into C i sensing. SbtB is highly conserved in cyanobacteria and is coexpressed with CCM genes. The SbtB protein from the cyanobacterium Synechocystis sp. PCC 6803 bound a variety of adenosine nucleotides, including the second messenger cAMP. Cocrystal structures unraveled the individual binding modes of trimeric SbtB with AMP and cAMP. The nucleotide-binding pocket is located between the subunit clefts of SbtB, perfectly matching the structure of canonical P II proteins. This clearly indicates that proteins of the P II superfamily arose from a common ancestor, whose structurally conserved nucleotide-binding pocket has evolved to sense different adenyl nucleotides for various signaling functions. Moreover, we provide physiological and biochemical evidence for the involvement of SbtB in C i acclimation. Collectively, our results suggest that SbtB acts as a C i sensor protein via cAMP binding, highlighting an evolutionarily conserved role for cAMP in signaling the cellular carbon status.


  • Organizational Affiliation

    Organismic Interactions Department, Interfaculty Institute for Microbiology and Infection Medicine, Tübingen University, 72076 Tübingen, Germany; khaled.selim@uni-tuebingen.de karl.forchhammer@uni-tuebingen.de.


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 6803 substr. KazusaMutation(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
Binding Affinity Annotations 
IDSourceBinding Affinity
CMP Binding MOAD:  5O3Q Kd: 2100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.386α = 90
b = 64.386β = 90
c = 81.459γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description