› 4s1b

X-ray diffraction
2.1Å resolution

Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with Cyclic-di-AMP

Released:
DOI: 10.2210/pdb4s1b/pdb
PDB entry 4s1b coloured by chain, front view.
PDB entry 4s1b coloured by chain, side view.
PDB entry 4s1b coloured by chain, top view.
Source organism: Listeria monocytogenes EGD-e
Primary publication:
An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.
Huynh TN, Luo S, Pensinger D, Sauer JD, Tong L, Woodward JJ
Proc Natl Acad Sci U S A 112 E747-56 (2015)
PMID: 25583510

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-186977 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
HD domain-containing protein Chains: A, D
Molecule details ›
Chains: A, D
Length: 222 amino acids
Theoretical weight: 25.12 KDa
Source organism: Listeria monocytogenes EGD-e
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8Y746 (Residues: 494-715; Coverage: 31%)
Gene name: lmo1466
Sequence domains: HD domain

Ligands and Environments

2 bound ligands:
Ligand FE 4 x FE
Ligand 2BA 2 x 2BA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P61
Unit cell:
a: 124.286Å b: 124.286Å c: 58.019Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.165 0.162 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

24 review citations

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

9 mentions without citation

Making and Breaking of an Essential Poison: the Cyclases and Phosphodiesterases That Produce and Degrade the Essential Second Messenger Cyclic di-AMP in Bacteria.
Commichau et al. (2019)
8 more