4C3K

Structure of mixed PII-ADP complexes from S. elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.099 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M113.536557
  • Primary Citation of Related Structures:  

  • 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 b ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROGEN REGULATORY PROTEIN P-II
A, B, C, D, E, F
115Synechococcus elongatus (strain PCC 7942)Mutation(s): 0 
Gene Names: glnB
Find proteins for P0A3F4 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  P0A3F4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.099 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 122.463α = 90.00
b = 122.463β = 90.00
c = 80.476γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references
  • Version 1.2: 2014-04-16
    Type: Database references