› 1ptm

X-ray diffraction
1.96Å resolution

Crystal structure of E.coli PdxA

Released:
DOI: 10.2210/pdb1ptm/pdb
PDB entry 1ptm coloured by chain, front view.
PDB entry 1ptm coloured by chain, side view.
PDB entry 1ptm coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway.
Sivaraman J, Li Y, Banks J, Cane DE, Matte A, Cygler M
J Biol Chem 278 43682-90 (2003)
PMID: 12896974

Function and Biology Details

Reaction catalysed: 
4-phosphooxy-L-threonine + NAD(+) = 3-amino-2-oxopropyl phosphate + CO(2) + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148671 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxythreonine-4-phosphate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 35.52 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P19624 (Residues: 1-329; Coverage: 100%)
Gene names: JW0051, b0052, pdxA
Sequence domains: Pyridoxal phosphate biosynthetic protein PdxA
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand PO4 1 x PO4
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: P212121
Unit cell:
a: 75.478Å b: 79.228Å c: 114.157Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.267
Expression system: Escherichia coli

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Citations

4 review citations

Vitamin B6: a long known compound of surprising complexity.
Mooney et al. (2009)
3 more

1 mention without citation

Geometric and electronic properties of AulPtm (l + m ≤ 10) clusters: a first-principles study.
Xie et al. (2021)