› 5e3p

X-ray diffraction
2.01Å resolution

Crystal structure of DapD from Corynebacterium glutamicum

Released:
DOI: 10.2210/pdb5e3p/pdb
PDB entry 5e3p coloured by chain, front view.
PDB entry 5e3p coloured by chain, side view.
PDB entry 5e3p coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
Primary publication:
Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum.
Sagong HY, Kim KJ
J Agric Food Chem 63 10641-6 (2015)
PMID: 26602189

Function and Biology Details

Reaction catalysed: 
Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H(2)O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185649 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 31.91 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8NRE3 (Residues: 2-297; Coverage: 100%)
Gene names: Cgl1106, cg1256, dapD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PG4 1 x PG4
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P6322
Unit cell:
a: 91.001Å b: 91.001Å c: 156.815Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.176 0.218
Expression system: Escherichia coli BL21

Quick links

Citations

1 citations in other articles

Reconstruction of the Diaminopimelic Acid Pathway to Promote L-lysine Production in Corynebacterium glutamicum.
Liu et al. (2021)