› 3fsx

X-ray diffraction
2.15Å resolution

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis

Released:
DOI: 10.2210/pdb3fsx/pdb
PDB entry 3fsx coloured by chain, front view.
PDB entry 3fsx coloured by chain, side view.
PDB entry 3fsx coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism.
Schuldt L, Weyand S, Kefala G, Weiss MS
J Mol Biol 389 863-79 (2009)
PMID: 19394346

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-161916 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 332 amino acids
Theoretical weight: 34.38 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WP21 (Residues: 2-317; Coverage: 100%)
Gene names: Rv1201c, dapD
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ACY 4 x ACY
Ligand MPD 3 x MPD
Ligand MG 9 x MG
Ligand NA 4 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: I213
Unit cell:
a: 216.99Å b: 216.99Å c: 216.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.168 0.219
Expression system: Escherichia coli

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Citations

1 review citation

Structure and function of Mycobacterium tuberculosis meso-diaminopimelic acid (DAP) biosynthetic enzymes.
Usha et al. (2012)
7 other articles

2 mentions without citation

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