Structural studies on Mycobacterium tuberculosis HddA enzyme using small angle X-ray scattering and dynamics simulation techniques

Sumita Karan^a, Ankita Behl^a, Amin Sagar^b, Arkita Bandyopadhyay^a, Ajay K.Saxena^a

Rm-403/440, Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

Abstract

Mycobacterium tuberculosis HddA enzyme phosphorylates the M7P substrate and converts it to M7PP product in GDP-D-α-D-heptose biosynthetic pathway. For structural and functional studies on MtbHddA, we have purified the enzyme, which eluted as a monomer from size exclusion column. Purified MtbHddA had ATPase activity. The SAXS analysis supported globular monomeric scattering profile of MtbHddA in solution. The CD analysis showed that MtbHddA contains 45% α-helix, 18% β-stands, and 32% random coil structures and showed unfolding temperature (T_M) ~ 47.5°C. The unfolding temperature of MtbHddA is enhanced by 1.78±0.41°C in ATP+Mg²⁺ bound state, 2.12±0.41°C in Mannose bound state and 3.07±0.41°C in Mannose+ ATP+Mg²⁺ bound state. The apo and M7P +ATP + Mg²⁺ complexed models of MtbHddA showed that enzyme adopts a classical GHMP sugar kinase fold with conserved ATP+Mg²⁺ and M7P binding sites. The dynamics simulation analysis on four MtbHddA models showed that ATP+Mg²⁺ and M7P binding enhanced the stability of active site conformation of MtbHddA. Our study provides important insights into MtbHddA structure and activity, which can be targeted for therapeutic development against M. tuberculosis.

Keywords: MtbHddA, ATPase assay, Circular dichroism, SAXS, Homology modeling, Dynamics simulation.