Hydrophobic Shielding Drives Catalysis of Hydride Transfer in a Family of F420H2-Dependent Enzymes

A. Elaaf Mohamed, Karmen Condic-Jurkic, F. Hafna Ahmed, Peng Yuan, Megan L. O'Mara, Colin J. Jackson, Michelle L. Coote

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

Abstract

A family of flavin/deazaflavin-dependent oxidoreductases (FDORs) from mycobacteria has been recently characterized and found to play a variety of catalytic roles, including the activation of prodrugs such as the candidate anti-tuberculosis drug pretomanid (PA-824). However, our understanding of the catalytic mechanism used by these enzymes is relatively limited. To address this, we have used a combination of quantum mechanics and molecular dynamics calculations to study the catalytic mechanism of the activation of pretomanid by the deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis. The preferred pathway involves an initial hydride transfer step from the deprotonated cofactor (i.e., F420H-), with subsequent protonation, before a series of spontaneous intramolecular reactions to form the final reactive nitrogen species. The most likely proton source is a hydroxonium ion within the solvent accessible active site. Intriguingly, catalysis of the rate-determining hydride transfer step is aided by three tyrosine residues that form a hydrophobic barrier around the active site that, upon reaction, is then disrupted to allow increased water accessibility to facilitate the subsequent proton transfer step. The catalytic mechanism we propose is consistent with previous experimental observations of the Ddn enzyme and will inform the design of improved prodrugs in the future.

Original languageEnglish
Pages (from-to)6908-6918
Number of pages11
JournalBiochemistry
Volume55
Issue number49
DOIs
Publication statusPublished - 13 Dec 2016
Externally publishedYes

Keywords

  • Hydride transfer
  • Peptides and proteins
  • Reaction mechanisms
  • Monomers
  • Energy

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