1ZAU

Adenylation domain of NAD+ dependent DNA ligase from M.tuberculosis

Summary for 1ZAU

• Entry DOI: 10.2210/pdb1zau/pdb
• Descriptor: DNA ligase, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: nad+ dependent dna ligase, amp, m.tuberculosis, ligase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 37126.24

Authors

Srivastava, S.K.,Ramachandran, R. (deposition date: 2005-04-07, release date: 2005-07-05, Last modification date: 2024-02-14)

Primary citation

Srivastava, S.K.,Tripathi, R.P.,Ramachandran, R.
NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis: CRYSTAL STRUCTURE OF THE ADENYLATION DOMAIN AND IDENTIFICATION OF NOVEL INHIBITORS
J.Biol.Chem., 280:30273-30281, 2005

PubMed Abstract: DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents.

PubMed: 15901723
DOI: 10.1074/jbc.M503780200

Experimental method

X-RAY DIFFRACTION (3.15 Å)