TY - JOUR
T1 - An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer
T2 - Through Proton-Coupled-Electron-Transfer
AU - Cao, Yuanxin
AU - Hay, Sam
AU - De Visser, Samuel
N1 - Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society.
PY - 2024/5/1
Y1 - 2024/5/1
N2 - Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about 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 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 regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C
4-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 C
4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C
4-H hydroxylation selectivity. Furthermore, an active site Tyr
233 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 Tyr
233 phenol loses a proton to the nearby Asp
179 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 C
4-H bond of the substrate and guides the selectivity to the C
4-hydroxylation of the substrate.
AB - Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about 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 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 regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C
4-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 C
4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C
4-H hydroxylation selectivity. Furthermore, an active site Tyr
233 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 Tyr
233 phenol loses a proton to the nearby Asp
179 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 C
4-H bond of the substrate and guides the selectivity to the C
4-hydroxylation of the substrate.
KW - Nonheme iron enzymes
KW - hydroxylation
KW - regioselectivity
KW - density functional theory
KW - cluster models
U2 - 10.1021/jacs.3c14574
DO - 10.1021/jacs.3c14574
M3 - Article
C2 - 38636166
SN - 0002-7863
VL - 146
SP - 11726
EP - 11739
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
IS - 17
ER -