› 5k2z

X-ray diffraction
1.8Å resolution

PDX1.3-adduct (Arabidopsis)

Released:
DOI: 10.2210/pdb5k2z/pdb
PDB entry 5k2z coloured by chain, front view.
PDB entry 5k2z coloured by chain, side view.
PDB entry 5k2z coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.
Robinson GC, Kaufmann M, Roux C, Fitzpatrick TB
Proc Natl Acad Sci U S A 113 E5821-E5829 (2016)
PMID: 27647886

Function and Biology Details

Reaction catalysed: 
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185267 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal 5'-phosphate synthase subunit PDX1.3 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 315 amino acids
Theoretical weight: 34.09 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8L940 (Residues: 1-309; Coverage: 100%)
Gene names: At5g01410, GIP2, PDX13, PDX1L3, RSR4, T10O8.120
Sequence domains: SOR/SNZ family
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand CL 2 x CL
Ligand SO4 8 x SO4
Ligand 6R3 4 x 6R3
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: R3
Unit cell:
a: 178.46Å b: 178.46Å c: 115.81Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.18 0.204
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

1 mention without citation

Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.
Robinson et al. (2016)