4LJ3

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with substrate c-di-GMP and Ca++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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). 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

    Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland. Electronic address: tilman.schirmer@unibas.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic di-GMP phosphodiesterase YahA
A, B
279Escherichia coli K-12Mutation(s): 0 
Gene Names: yahAb0315JW0307
EC: 3.1.4
UniProt
Find proteins for P21514 (Escherichia coli (strain K12))
Explore P21514 
Go to UniProtKB:  P21514
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21514
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
HB0
Query on HB0

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
trans-4-(hydroxymethyl)cyclohexanol
C7 H14 O2
VGRZISGVNOKTQU-LJGSYFOKSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E Binding MOAD:  4LJ3 Kd: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.693α = 90
b = 70.3β = 98.68
c = 66.636γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary