› 3du0

X-ray diffraction
2Å resolution

E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site

Released:
DOI: 10.2210/pdb3du0/pdb
PDB entry 3du0 coloured by chain, front view.
PDB entry 3du0 coloured by chain, side view.
PDB entry 3du0 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate.
Devenish SR, Gerrard JA, Jameson GB, Dobson RC
Acta Crystallogr Sect F Struct Biol Cryst Commun 64 1092-5 (2008)
PMID: 19052357

Function and Biology Details

Reaction catalysed: 
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141377 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 292 amino acids
Theoretical weight: 31.37 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6L2 (Residues: 1-292; Coverage: 100%)
Gene names: JW2463, b2478, dapA
Sequence domains: Dihydrodipicolinate synthetase family
Structure domains: Aldolase class I

Ligands and Environments

3 bound ligands:
Ligand K 4 x K
Ligand GOL 3 x GOL
Ligand CL 4 x CL
1 modified residue:
Ligand KPI 2 x KPI

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P3121
Unit cell:
a: 120.95Å b: 120.95Å c: 110.03Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.188 0.245
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition.
Atkinson et al. (2013)
2 more

8 mentions without citation

Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method.
Naz et al. (2023)
7 more