› 4lyk

X-ray diffraction
2.4Å resolution

Crystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++

Released:
DOI: 10.2210/pdb4lyk/pdb
Model geometry
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Source organism: Escherichia coli K-12
Primary publication:
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
J Biol Chem 289 6978-6990 (2014)
PMID: 24451384

Function and Biology Details

Reaction catalysed: 
Cyclic di-3',5'-guanylate + H(2)O = 5'-phosphoguanylyl(3'->5')guanosine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-149278 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic di-GMP phosphodiesterase PdeL Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 279 amino acids
Theoretical weight: 31.08 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21514 (Residues: 101-362; Coverage: 72%)
Gene names: JW0307, b0315, pdeL, yahA
Sequence domains: EAL domain
Structure domains: EAL domain

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand HB0 4 x HB0
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 64.85Å b: 109.547Å c: 81.75Å
α: 90° β: 99.39° γ: 90°
R-values:
R R work R free
0.19 0.189 0.222
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Cyclic di-GMP: second messenger extraordinaire.
Jenal et al. (2017)
5 more

4 mentions without citation

Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP.
Sundriyal et al. (2014)
3 more

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