4KIE

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inherent Regulation of EAL Domain-catalyzed Hydrolysis of Second Messenger Cyclic di-GMP.

Sundriyal, A.Massa, C.Samoray, D.Zehender, F.Sharpe, T.Jenal, U.Schirmer, T.

(2014) J Biol Chem 289: 6978-6990

  • DOI: 10.1074/jbc.M113.516195
  • Primary Citation of Related Structures:  
    4KIE, 4LJ3, 4LYK

  • PubMed Abstract: 
  • The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases and cdG-specific phosphodiesterases (PDEs) ...

    The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases and cdG-specific phosphodiesterases (PDEs). Whereas most PDEs have accessory domains that are involved in the regulation of their activity, the regulatory mechanism of this class of enzymes has remained unclear. Here, we use biophysical and functional analyses to show that the isolated EAL domain of a PDE from Escherichia coli (YahA) is in a fast thermodynamic monomer-dimer equilibrium, and that the domain is active only in its dimeric state. Furthermore, our data indicate thermodynamic coupling between substrate binding and EAL dimerization with the dimerization affinity being increased about 100-fold upon substrate binding. Crystal structures of the YahA-EAL domain determined under various conditions (apo, Mg(2+), cdG·Ca(2+) complex) confirm structural coupling between the dimer interface and the catalytic center. The built-in regulatory properties of the EAL domain probably facilitate its modular, functional combination with the diverse repertoire of accessory domains.


    Organizational Affiliation

    From the Focal Area of Structural Biology and Biophysics.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclic di-GMP phosphodiesterase YahAA279Escherichia coli K-12Mutation(s): 0 
Gene Names: yahAb0315JW0307pdeL
EC: 3.1.4 (PDB Primary Data), 3.1.4.52 (UniProt)
UniProt
Find proteins for P21514 (Escherichia coli (strain K12))
Explore P21514 
Go to UniProtKB:  P21514
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.626α = 90
b = 87.818β = 90
c = 94.723γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references, Other
  • Version 1.2: 2014-05-14
    Changes: Database references