› 3r5c

X-ray diffraction
2.4Å resolution

Pseudomonas aeruginosa DapD (PA3666) in complex with CoA and succinate

Released:
DOI: 10.2210/pdb3r5c/pdb
PDB entry 3r5c coloured by chain, front view.
PDB entry 3r5c coloured by chain, side view.
PDB entry 3r5c coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Schnell R, Oehlmann W, Sandalova T, Braun Y, Huck C, Maringer M, Singh M, Schneider G
OpenAccess logo PLoS One 7 e31133 (2012)
PMID: 22359568

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-124408 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 347 amino acids
Theoretical weight: 36.29 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: G3XD76 (Residues: 1-344; Coverage: 100%)
Gene names: PA3666, dapD
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand COA 3 x COA
1 bound ligand:
Ligand SIN 3 x SIN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P41212
Unit cell:
a: 123.282Å b: 123.282Å c: 198.763Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.267
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Dissociative mechanism for irreversible thermal denaturation of oligomeric proteins.
Chebotareva et al. (2016)
1 more

1 mention without citation

Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Schnell et al. (2012)