› 5xsp

X-ray diffraction
2.15Å resolution

The catalytic domain of GdpP with 5'-pApA

Released:
DOI: 10.2210/pdb5xsp/pdb
PDB entry 5xsp coloured by chain, front view.
PDB entry 5xsp coloured by chain, side view.
PDB entry 5xsp coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase.
Wang F, He Q, Su K, Wei T, Xu S, Gu L
Biochem J 475 191-205 (2018)
PMID: 29203646

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102714 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic-di-AMP phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 343 amino acids
Theoretical weight: 38.13 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0U1MUE2 (Residues: 322-661; Coverage: 51%)
Gene names: BN1321_430104, cdnD
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand MN 4 x MN
Ligand A 4 x A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 54.619Å b: 117.263Å c: 127.368Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.243
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)
8 other articles

3 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)
2 more