› 5t9c

X-ray diffraction
1.48Å resolution

Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour soak)

Released:
DOI: 10.2210/pdb5t9c/pdb
PDB entry 5t9c coloured by chain, front view.
PDB entry 5t9c coloured by chain, side view.
PDB entry 5t9c coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component.
Myers CL, Li FK, Koo BM, El-Halfawy OM, French S, Gross CA, Strynadka NC, Brown ED
J Biol Chem 291 26066-26082 (2016)
PMID: 27780866

Function and Biology Details

Reaction catalysed: 
A glycerophosphodiester + H(2)O = an alcohol + sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153524 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphodiester phosphodiesterase Chain: E
Molecule details ›
Chain: E
Length: 268 amino acids
Theoretical weight: 30.2 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37965 (Residues: 27-293; Coverage: 100%)
Gene names: BSU02130, glpQ, ybeD
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand G3P 1 x G3P
Ligand PO4 1 x PO4
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 47.101Å b: 58.24Å c: 87.565Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.197
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Activation of the PhoPR-Mediated Response to Phosphate Limitation Is Regulated by Wall Teichoic Acid Metabolism in Bacillus subtilis.
Devine KM. (2018)
5 more

4 mentions without citation

Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component.
Myers et al. (2016)
3 more