› 6ecd

X-ray diffraction
1.9Å resolution

Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide

Released:
DOI: 10.2210/pdb6ecd/pdb
PDB entry 6ecd coloured by chain, front view.
PDB entry 6ecd coloured by chain, side view.
PDB entry 6ecd coloured by chain, top view.
Source organisms:
Primary publication:
Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.
Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW
Nature 565 112-117 (2019)
PMID: 30542153

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166657 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Carrier domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 303 amino acids
Theoretical weight: 33.1 KDa
Source organism: Streptomyces tsusimaensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1PSF3 (Residues: 2368-2655; Coverage: 11%)
Gene name: vlm2
Sequence domains: Thioesterase domain
tetradepsipeptide Chain: B
Molecule details ›
Chain: B
Length: 4 amino acids
Theoretical weight: 388 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
3 modified residues:
Ligand DPP 1 x DPP
Ligand VAD 1 x VAD
Ligand DVA 1 x DVA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P432
Unit cell:
a: 152.298Å b: 152.298Å c: 152.298Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.214
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Reprogramming the genetic code.
de la Torre et al. (2021)
5 more

2 mentions without citation

Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases.
Patel et al. (2023)
1 more