Structure of mixed PII-ADP complexes from S. elongatus

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Structural Basis and Target-Specific Modulation of Adp Sensing by the Synechococcus Elongatus Pii Signaling Protein.

Zeth, K.Fokina, O.Forchhammer, K.

(2014) J Biol Chem 289: 8960

  • DOI: https://doi.org/10.1074/jbc.M113.536557
  • Primary Citation of Related Structures:  
    4C3K, 4C3L, 4C3M

  • PubMed Abstract: 

    PII signaling proteins comprise one of the most versatile signaling devices in nature and have a highly conserved structure. In cyanobacteria, PipX and N-acetyl-L-glutamate kinase are receptors of PII signaling, and these interactions are modulated by ADP, ATP, and 2-oxoglutarate. These effector molecules bind interdependently to three anti-cooperative binding sites on the trimeric PII protein and thereby affect its structure. Here we used the PII protein from Synechococcus elongatus PCC 7942 to reveal the structural basis of anti-cooperative ADP binding. Furthermore, we clarified the mutual influence of PII-receptor interaction and sensing of the ATP/ADP ratio. The crystal structures of two forms of trimeric PII, one with one ADP bound and the other with all three ADP-binding sites occupied, revealed significant differences in the ADP binding mode: at one site (S1) ADP is tightly bound through side-chain and main-chain interactions, whereas at the other two sites (S2 and S3) the ADP molecules are only bound by main-chain interactions. In the presence of the PII-receptor PipX, the affinity of ADP to the first binding site S1 strongly increases, whereas the affinity for ATP decreases due to PipX favoring the S1 conformation of PII-ADP. In consequence, the PII-PipX interaction is highly sensitive to subtle fluctuations in the ATP/ADP ratio. By contrast, the PII-N-acetyl-L-glutamate kinase interaction, which is negatively affected by ADP, is insensitive to these fluctuations. Modulation of the metabolite-sensing properties of PII by its receptors allows PII to differentially perceive signals in a target-specific manner and to perform multitasking signal transduction.

  • Organizational Affiliation

    From the Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tübingen, Germany and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
115Synechococcus elongatusMutation(s): 0 
Find proteins for P0A3F4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore P0A3F4 
Go to UniProtKB:  P0A3F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3F4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.463α = 90
b = 122.463β = 90
c = 80.476γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description