› 3vmm

X-ray diffraction
2.5Å resolution

Crystal structure of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis

Released:
DOI: 10.2210/pdb3vmm/pdb
PDB entry 3vmm coloured by chain, front view.
PDB entry 3vmm coloured by chain, side view.
PDB entry 3vmm coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis.
Shomura Y, Hinokuchi E, Ikeda H, Senoo A, Takahashi Y, Saito J, Komori H, Shibata N, Yonetani Y, Higuchi Y
Protein Sci 21 707-16 (2012)
PMID: 22407814

Function and Biology Details

Reaction catalysed: 
ATP + L-alanine + L-anticapsin = ADP + phosphate + bacilysin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153916 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alanine--anticapsin ligase Chain: A
Molecule details ›
Chain: A
Length: 474 amino acids
Theoretical weight: 52.45 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P39641 (Residues: 1-472; Coverage: 100%)
Gene names: BSU37710, bacD, ipa-83d, ywfE
Sequence domains: ATP-grasp domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ADP 1 x ADP
Ligand P0D 1 x P0D
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P6522
Unit cell:
a: 130.787Å b: 130.787Å c: 147.742Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.229
Expression system: Escherichia coli

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Citations

4 review citations

Current topics in the biotechnological production of essential amino acids, functional amino acids, and dipeptides.
Mitsuhashi S. (2014)
3 more

4 mentions without citation

Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry.
Wang et al. (2019)
3 more