› 3wnz

X-ray diffraction
1.9Å resolution

Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Pi

Released:
DOI: 10.2210/pdb3wnz/pdb
PDB entry 3wnz coloured by chain, front view.
PDB entry 3wnz coloured by chain, side view.
PDB entry 3wnz coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Single mutation alters the substrate specificity of L-amino acid ligase.
Tsuda T, Asami M, Koguchi Y, Kojima S
Biochemistry 53 2650-60 (2014)
PMID: 24702628

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153917 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alanine--anticapsin ligase Chain: A
Molecule details ›
Chain: A
Length: 470 amino acids
Theoretical weight: 51.91 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: P39641 (Residues: 4-468; Coverage: 99%)
Gene names: BSU37710, bacD, ipa-83d, ywfE
Sequence domains: ATP-grasp domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ADP 1 x ADP
Ligand MG 2 x MG
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P6522
Unit cell:
a: 90.581Å b: 90.581Å c: 252.654Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.197 0.243
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome.
Goswami et al. (2015)
5 more