› 4me6

X-ray diffraction
2.1Å resolution

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Released:
DOI: 10.2210/pdb4me6/pdb
PDB entry 4me6 coloured by chain, front view.
PDB entry 4me6 coloured by chain, side view.
PDB entry 4me6 coloured by chain, top view.
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Primary publication:
Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.
Doan TT, Kim JK, Ngo HP, Tran HT, Cha SS, Min Chung K, Huynh KH, Ahn YJ, Kang LW
Arch Biochem Biophys 545 92-9 (2014)
PMID: 24440607

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177168 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chain: A
Molecule details ›
Chain: A
Length: 386 amino acids
Theoretical weight: 41.95 KDa
Source organism: Xanthomonas oryzae pv. oryzae KACC 10331
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5H614 (Residues: 1-347; Coverage: 100%)
Gene names: XOO0352, ddl, ddlA
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P43212
Unit cell:
a: 83.236Å b: 83.236Å c: 98.277Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.192 0.251
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae.
Borah et al. (2020)
3 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)