6KKV

Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis

Summary for 6KKV

• Entry DOI: 10.2210/pdb6kkv/pdb
• Descriptor: DNA ligase A, N-[(4-methylphenyl)methyl]-1H-pyrrole-2-carboxamide, SULFATE ION, ... (4 entities in total)
• Functional Keywords: ligase
• Biological source: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Total number of polymer chains: 1
• Total formula weight: 37310.55

Authors

Ramachandran, R.,Shukla, A.,Afsar, M. (deposition date: 2019-07-27, release date: 2020-07-29, Last modification date: 2023-11-22)

Primary citation

Shukla, A.,Afsar, M.,Kumar, N.,Kumar, S.,Ramachandran, R.
Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD + -dependent DNA ligase A.
J.Struct.Biol., 213:107655-107655, 2021

PubMed Abstract: NAD-dependent DNA ligase (LigA) is the essential replicative ligase in bacteria and differs from ATP-dependent counterparts like the human DNA ligase I (HligI) in several aspects. LigA uses NAD as the co-factor while the latter uses ATP. Further, the LigA carries out enzymatic activity with a single divalent metal ion in the active site while ATP-dependent ligases use two metal ions. Instead of the second metal ion, LigA have a unique NMN binding subdomain that facilitates the orientation of the β-phosphate and NMN leaving group. LigA are therefore attractive targets for new anti-bacterial therapeutic development. Others and our group have earlier identified several LigA inhibitors that mainly bind to AMP binding site of LigA. However, no inhibitor is known to bind to the unique NMN binding subdomain. We initiated a fragment inhibitor discovery campaign against the M. tuberculosis LigA based on our co-crystal structure of adenylation domain with AMP and NMN. The study identified two fragments, 4-(4-fluorophenyl)-4,5,6,7-tetrahydro-3H imidazo[4,5-c] pyridine and N-(4-methylbenzyl)-1H-pyrrole-2-carboxamide, that bind to the NMN site. The fragments inhibit LigA with IC of 16.9 and 28.7 µM respectively and exhibit MIC of ~20 and 60 µg/ml against a temperature sensitive E. coli GR501 ligA strain, rescued by MtbLigA. Co-crystal structures of the fragments with the adenylation domain of LigA show that they mimic the interactions of NMN. Overall, our results suggest that the NMN binding-site is a druggable target site for developing anti-LigA therapeutic strategies.

PubMed: 33197566
DOI: 10.1016/j.jsb.2020.107655

Experimental method

X-RAY DIFFRACTION (2.56 Å)