1IOV: Complex of D-ala:d-ala Ligase With ADP and a Phosphoryl Phosphonate

Citation:
Abstract
The crystallographic structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli complexed with a D-Ala-D-alpha-hydroxybutyrate phosphonate and the structure of the Y216F mutant ligase complexed with a D-Ala-D-Ala phosphinate have been determined to 2.2 and 1.9 A resolution, respectively, and refined to R factors of 0.156 and 0.158. In each complex the inhibitor has reacted with ATP to produce ADP and a tight-binding phosphorylated transition state intermediate. Comparison of these two structures with the known crystal structure of the phosphinate intermediate of the wild-type ligase shows no major conformational changes, but B factors indicate differences in mobility of loops covering the binding site. The weaker inhibition of the Y216F mutant by both inhibitors is thought to be due in part to the loss of an interloop hydrogen bond. A similar mechanism may account for poor inhibition of VanA, the homologous D-Ala:D-lactate ligase produced by vancomycin-resistant enterococci.
PDB ID: 1IOVDownload
MMDB ID: 56458
PDB Deposition Date: 1996/9/20
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.2  Å
Source Organism:
Similar Structures:
Biological Unit for 1IOV: monomeric; determined by author
Molecular Components in 1IOV
Label Count Molecule
Protein (1 molecule)
1
D-ala:d-ala Ligase(Gene symbol: ddlB)
Molecule annotation
Chemicals (5 molecules)
1
3
2
1
3
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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