› 4wy0

X-ray diffraction
2.3Å resolution

PdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.

Released:
DOI: 10.2210/pdb4wy0/pdb
PDB entry 4wy0 coloured by chain, front view.
PDB entry 4wy0 coloured by chain, side view.
PDB entry 4wy0 coloured by chain, top view.
Source organism: Geobacillus kaustophilus HTA426
Primary publication:
Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase.
Smith AM, Brown WC, Harms E, Smith JL
J Biol Chem 290 5226-39 (2015)
PMID: 25568319

Function and Biology Details

Reaction catalysed: 
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177432 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pyridoxal 5'-phosphate synthase subunit PdxS Chains: A, C, E, G, I, J, K, L
Molecule details ›
Chains: A, C, E, G, I, J, K, L
Length: 305 amino acids
Theoretical weight: 33.12 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5L3Y2 (Residues: 1-294; Coverage: 100%)
Gene names: GK0011, pdxS
Sequence domains: SOR/SNZ family
Structure domains: Aldolase class I
Pyridoxal 5'-phosphate synthase subunit PdxS Chains: B, D, H
Molecule details ›
Chains: B, D, H
Length: 305 amino acids
Theoretical weight: 32.9 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5L3Y2 (Residues: 1-294; Coverage: 100%)
Gene names: GK0011, pdxS
Sequence domains: SOR/SNZ family
Structure domains: Aldolase class I
Pyridoxal 5'-phosphate synthase subunit PdxS Chain: F
Molecule details ›
Chain: F
Length: 304 amino acids
Theoretical weight: 32.93 KDa
Source organism: Geobacillus kaustophilus HTA426
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5L3Y2 (Residues: 1-294; Coverage: 100%)
Gene names: GK0011, pdxS
Sequence domains: SOR/SNZ family
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand CAC 5 x CAC
Ligand PO4 4 x PO4
Ligand R5P 7 x R5P
Ligand EDO 3 x EDO
1 modified residue:
Ligand L5P 8 x L5P

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 94.68Å b: 107.198Å c: 178.215Å
α: 90° β: 92.24° γ: 90°
R-values:
R R work R free
0.193 0.191 0.222
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Vitamin B₆ and Its Role in Cell Metabolism and Physiology.
Parra et al. (2018)
2 more

4 mentions without citation

Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions.
Barra et al. (2021)
3 more