1iov

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1iov, resolution 2.20Å ()
Ligands: , ,
Activity: D-alanine--D-alanine ligase, with EC number 6.3.2.4
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



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

Publication Abstract from PubMed

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.

D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant., Fan C, Park IS, Walsh CT, Knox JR, Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:9054558

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1iov is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

  • Fan C, Park IS, Walsh CT, Knox JR. D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant. Biochemistry. 1997 Mar 4;36(9):2531-8. PMID:9054558 doi:10.1021/bi962431t
  • Lee JH, Na Y, Song HE, Kim D, Park BH, Rho SH, Im YJ, Kim MK, Kang GB, Lee DS, Eom SH. Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes. Proteins. 2006 Sep 1;64(4):1078-82. PMID:16779845 doi:http://dx.doi.org/10.1002/prot.20927

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