3LWB

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis

Summary for 3LWB

• Entry DOI: 10.2210/pdb3lwb/pdb
• Descriptor: D-alanine--D-alanine ligase, NITRATE ION (3 entities in total)
• Functional Keywords: d-alanine--d-alanine ligase, ddl, d-alanyl--d-alanine ligase, rv2981c, d-alanine, structural genomics, tb structural genomics consortium, tbsgc, atp-binding, cell shape, cell wall biogenesis, degradation, ligase, magnesium, manganese, metal-binding, nucleotide-binding, peptidoglycan synthesis
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 79632.35

Authors

Bruning, J.B.,Murillo, A.C.,Chacon, O.,Barletta, R.G.,Sacchettini, J.C.,TB Structural Genomics Consortium (TBSGC) (deposition date: 2010-02-23, release date: 2010-03-09, Last modification date: 2023-09-06)

Primary citation

Bruning, J.B.,Murillo, A.C.,Chacon, O.,Barletta, R.G.,Sacchettini, J.C.
Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine.
Antimicrob.Agents Chemother., 55:291-301, 2011

PubMed 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 Å. 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(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.

PubMed: 20956591
DOI: 10.1128/AAC.00558-10

Experimental method

X-RAY DIFFRACTION (2.1 Å)