› 2pvp

X-ray diffraction
2.4Å resolution

Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori

Released:
DOI: 10.2210/pdb2pvp/pdb
PDB entry 2pvp coloured by chain, front view.
PDB entry 2pvp coloured by chain, side view.
PDB entry 2pvp coloured by chain, top view.
Source organism: Helicobacter pylori SS1
Primary publication:
Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori.
Wu D, Zhang L, Kong Y, Du J, Chen S, Chen J, Ding J, Jiang H, Shen X
Proteins 72 1148-60 (2008)
PMID: 18320587

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-173846 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 367 amino acids
Theoretical weight: 41.96 KDa
Source organism: Helicobacter pylori SS1
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q2N4T5 (Residues: 1-347; Coverage: 100%)
Gene name: ddl
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 70.969Å b: 89.016Å c: 121.883Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.229 0.283
Expression system: Escherichia coli BL21

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Citations

11 citation in other articles

Remarkable potential of the α-aminophosphonate/phosphinate structural motif in medicinal chemistry.
Mucha et al. (2011)
10 more

3 mentions without citation

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Li et al. (2020)
2 more