1IOW

COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE

Summary for 1IOW

• Entry DOI: 10.2210/pdb1iow/pdb
• Descriptor: D-ALA\:D-ALA LIGASE, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: glycogen phosphorylase, ligase, cell wall, peptidoglycan synthesis, vancomycin, adp binding
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P07862
• Total number of polymer chains: 1
• Total formula weight: 33602.54

Authors

Knox, J.R.,Moews, P.C.,Fan, C. (deposition date: 1996-09-20, release date: 1997-02-12, Last modification date: 2024-05-22)

Primary citation

Fan, C.,Park, I.S.,Walsh, C.T.,Knox, J.R.
D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.
Biochemistry, 36:2531-2538, 1997

PubMed 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.

PubMed: 9054558
DOI: 10.1021/bi962431t

Experimental method

X-RAY DIFFRACTION (1.9 Å)