› 5lns

X-ray diffraction
1.91Å resolution

Crystal structure of Arabidopsis thaliana Pdx1-R5P complex

Released:
DOI: 10.2210/pdb5lns/pdb
PDB 5lns coloured by chain and viewed from the front.
PDB 5lns coloured by chain and viewed from the side.
PDB 5lns coloured by chain and viewed from the top.
Source organism: Arabidopsis thaliana
Primary publication:
Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.
Rodrigues MJ, Windeisen V, Zhang Y, Guédez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I
Nat Chem Biol 13 290-294 (2017)
PMID: 28092359

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)
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: 316 amino acids
Theoretical weight: 34.22 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
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

2 bound ligands:
Ligand 5RP 4 x 5RP
Ligand PO4 4 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: R3
Unit cell:
a: 176.728Å b: 176.728Å c: 114.646Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.16 0.158 0.189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Vitamin B₆ and Its Role in Cell Metabolism and Physiology.
Parra et al. (2018)
3 other articles