Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine
Abstract
D-Alanine:D-alanine ligase (EC 6.3.2.4; Ddl) catalyzes the ATP-driven ligation of two D-alanine (D-Ala) molecules to form the D-alanyl:D-alanine dipeptide. This molecule is a key building block in peptidoglycan biosynthesis, making Ddl an attractive target for drug development. D-Cycloserine (DCS), an analog of D-Ala and a prototype Ddl inhibitor, has shown promise for the treatment of tuberculosis. Here, we report the crystal structure of Mycobacterium tuberculosis Ddl at a resolution of 2.1 {angstrom}. This structure indicates that Ddl is a dimer and consists of three discrete domains; the ligand binding cavity is at the intersection of all three domains and conjoined by several loop regions. The M. tuberculosis apo Ddl structure shows a novel conformation that has not yet been observed in Ddl enzymes from other species. The nucleotide and D-alanine binding pockets are flexible, requiring significant structural rearrangement of the bordering regions for entry and binding of both ATP and D-Ala molecules. Solution affinity and kinetic studies showed that DCS interacts with Ddl in a manner similar to that observed for D-Ala. Each ligand binds to two binding sites that have significant differences in affinity, with the first binding site exhibiting high affinity. DCS inhibits the enzyme, with a 50%more »
- Authors:
-
- TAM
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- OTHERUNIVERSITYUSDANIH
- OSTI Identifier:
- 1023659
- Resource Type:
- Journal Article
- Journal Name:
- Antimicrob. Agents Ch.
- Additional Journal Information:
- Journal Volume: 55; Journal Issue: (1) ; 01, 2011; Journal ID: ISSN 0066-4804
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; AFFINITY; ATP; BIOSYNTHESIS; CRYSTAL STRUCTURE; DIMERS; DRUGS; ENZYMES; INHIBITION; KINETICS; LIGANDS; LIGASES; MOLECULES; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDES; POTENTIALS; RESOLUTION; TARGETS
Citation Formats
Bruning, John B, Murillo, Ana C, Chacon, Ofelia, Barletta, Raúl G, Sacchettini, James C, and UNL). Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine. United States: N. p., 2011.
Web. doi:10.1128/AAC.00558-10.
Bruning, John B, Murillo, Ana C, Chacon, Ofelia, Barletta, Raúl G, Sacchettini, James C, & UNL). Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine. United States. https://doi.org/10.1128/AAC.00558-10
Bruning, John B, Murillo, Ana C, Chacon, Ofelia, Barletta, Raúl G, Sacchettini, James C, and UNL). 2011.
"Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine". United States. https://doi.org/10.1128/AAC.00558-10.
@article{osti_1023659,
title = {Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine},
author = {Bruning, John B and Murillo, Ana C and Chacon, Ofelia and Barletta, Raúl G and Sacchettini, James C and UNL)},
abstractNote = {D-Alanine:D-alanine ligase (EC 6.3.2.4; Ddl) catalyzes the ATP-driven ligation of two D-alanine (D-Ala) molecules to form the D-alanyl:D-alanine dipeptide. This molecule is a key building block in peptidoglycan biosynthesis, making Ddl an attractive target for drug development. D-Cycloserine (DCS), an analog of D-Ala and a prototype Ddl inhibitor, has shown promise for the treatment of tuberculosis. Here, we report the crystal structure of Mycobacterium tuberculosis Ddl at a resolution of 2.1 {angstrom}. This structure indicates that Ddl is a dimer and consists of three discrete domains; the ligand binding cavity is at the intersection of all three domains and conjoined by several loop regions. The M. tuberculosis apo Ddl structure shows a novel conformation that has not yet been observed in Ddl enzymes from other species. The nucleotide and D-alanine binding pockets are flexible, requiring significant structural rearrangement of the bordering regions for entry and binding of both ATP and D-Ala molecules. Solution affinity and kinetic studies showed that DCS interacts with Ddl in a manner similar to that observed for D-Ala. Each ligand binds to two binding sites that have significant differences in affinity, with the first binding site exhibiting high affinity. DCS inhibits the enzyme, with a 50% inhibitory concentration (IC{sub 50}) of 0.37 mM under standard assay conditions, implicating a preferential and weak inhibition at the second, lower-affinity binding site. Moreover, DCS binding is tighter at higher ATP concentrations. The crystal structure illustrates potential drugable sites that may result in the development of more-effective Ddl inhibitors.},
doi = {10.1128/AAC.00558-10},
url = {https://www.osti.gov/biblio/1023659},
journal = {Antimicrob. Agents Ch.},
issn = {0066-4804},
number = (1) ; 01, 2011,
volume = 55,
place = {United States},
year = {Wed Sep 28 00:00:00 EDT 2011},
month = {Wed Sep 28 00:00:00 EDT 2011}
}