6URF

Malic enzyme from Mycobacterium tuberculosis

Summary for 6URF

• Entry DOI: 10.2210/pdb6urf/pdb
• Descriptor: NAD-dependent malic enzyme, GLYCEROL (3 entities in total)
• Functional Keywords: malic enzyme, fatty acid synthesis, glucose metabolism, cytosolic protein, oxidoreductase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 4
• Total formula weight: 248624.78

Authors

Cuthbert, B.J.,Burley, K.H.,Goulding, C.W.,Mathews, E.I.,Beste, D.J. (deposition date: 2019-10-23, release date: 2020-10-28, Last modification date: 2023-10-11)

Primary citation

Burley, K.H.,Cuthbert, B.J.,Basu, P.,Newcombe, J.,Irimpan, E.M.,Quechol, R.,Foik, I.P.,Mobley, D.L.,Beste, D.J.V.,Goulding, C.W.
Structural and Molecular Dynamics of Mycobacterium tuberculosis Malic Enzyme, a Potential Anti-TB Drug Target.
Acs Infect Dis., 7:174-188, 2021

PubMed Abstract: Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ contributes to lipid biosynthesis by providing reductants in the form of NAD(P)H. Here, we present the X-ray crystal structure of MEZ to 3.6 Å. We use biochemical assays to demonstrate MEZ is dimeric in solution and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn and NAD(P), we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually flexible, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that dimeric MEZ subunits alternate between open and closed states, and that MEZ can stably bind its NAD(P) cofactor in multiple conformations, including an inactive, compact NAD form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb and not human malic enzyme homologues.

PubMed: 33356117
DOI: 10.1021/acsinfecdis.0c00735

Experimental method

X-RAY DIFFRACTION (3.6 Å)