› 5nm8

X-ray diffraction
1.93Å resolution

Structure of PipY, the COG0325 family member of Synechococcus elongatus PCC7942, with PLP bound

Released:
DOI: 10.2210/pdb5nm8/pdb
PDB 5nm8 coloured by chain and viewed from the front.
PDB 5nm8 coloured by chain and viewed from the side.
PDB 5nm8 coloured by chain and viewed from the top.
Source organism: Synechococcus elongatus PCC 7942 = FACHB-805
Primary publication:
Studies on cyanobacterial protein PipY shed light on structure, potential functions, and vitamin B6 -dependent epilepsy.
Tremiño L, Forcada-Nadal A, Contreras A, Rubio V
FEBS Lett 591 3431-3442 (2017)
PMID: 28914444

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal phosphate homeostasis protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 228 amino acids
Theoretical weight: 25.3 KDa
Source organism: Synechococcus elongatus PCC 7942 = FACHB-805
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q31LH9 (Residues: 1-221; Coverage: 100%)
Gene name: Synpcc7942_2060
Sequence domains: Alanine racemase, N-terminal domain
Structure domains: Alanine racemase

Ligands and Environments

2 bound ligands:
Ligand PLP 2 x PLP
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 46.627Å b: 98.937Å c: 103.737Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.238
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis.
Richts et al. (2021)
3 more

1 mention without citation

Conserved Pyridoxal 5'-Phosphate-Binding Protein YggS Impacts Amino Acid Metabolism through Pyridoxine 5'-Phosphate in Escherichia coli.
Ito et al. (2019)