5O3R | pdb_00005o3r

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.207 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5O3R

Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 40.77 kDa 
  • Atom Count: 2,506 
  • Modeled Residue Count: 296 
  • Deposited Residue Count: 360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 ATCC 27184 / 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.207 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.425α = 90
b = 64.425β = 90
c = 80.737γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-10-23
    Changes: Structure summary