An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by the Nonheme Iron Lysine-4-Hydroxylase enzymes: Through Proton-Coupled-Electron-Transfer

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Abstract

Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen crosslinking and blood pressure control. There are several KDOs in Nature; however, little is known on the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of a 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B and C) containing 297, 312 and 407 atoms, respectively. The largest model predicts a regioselectivity that matches experimental observation with a rate-determining hydrogen atom abstraction from the C4−H position followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in Model C the dipole moment is positioned along the C4−H bond of the substrate and therefore the electrostatic and electric field perturbations of the protein assist the enzyme in creating a C4−H hydroxylation selectivity. Furthermore, an active site Tyr233 residue is identified that reacts through proton-coupled-electron-transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233 phenol loses a proton to the nearby Asp179 residue, while at the same time an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4−H bond of the substrate and guides the selectivity to C4-hydroxylation of the substrate.
Original languageEnglish
JournalJournal of the American Chemical Society
DOIs
Publication statusPublished - 18 Apr 2024

Keywords

  • Nonheme iron enzymes
  • hydroxylation
  • regioselectivity
  • density functional theory
  • cluster models

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