› 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 4s1b coloured by chain and viewed from the front.
PDB 4s1b coloured by chain and viewed from the side.
PDB 4s1b coloured by chain and viewed from the top.
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. (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
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)

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Citations

18 review citations

Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis.
Bowen et al. (2022)
17 more

9 mentions without citation

Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases.
Galperin et al. (2022)
8 more