› 5nrh

X-ray diffraction
1.3Å resolution

Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP

Released:
DOI: 10.2210/pdb5nrh/pdb
PDB entry 5nrh coloured by chain, front view.
PDB entry 5nrh coloured by chain, side view.
PDB entry 5nrh coloured by chain, top view.
Source organism: Burkholderia pseudomallei
Primary publication:
Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target.
Díaz-Sáez L, Torrie LS, McElroy SP, Gray D, Hunter WN
OpenAccess logo FEBS J 286 4509-4524 (2019)
PMID: 31260169

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179070 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 312 amino acids
Theoretical weight: 33.38 KDa
Source organism: Burkholderia pseudomallei
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q63QJ9 (Residues: 1-312; Coverage: 100%)
Gene names: BPSL3023, ddl
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand AMP 2 x AMP
Ligand MG 1 x MG
Ligand SO4 2 x SO4
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 69.648Å b: 61.15Å c: 70.079Å
α: 90° β: 90.17° γ: 90°
R-values:
R R work R free
0.148 0.146 0.19
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Structures and function of the amino acid polymerase cyanophycin synthetase.
Sharon et al. (2021)
1 more

1 mention without citation

Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target.
Díaz-Sáez et al. (2019)