Vitamin D3 Activation by Cytochrome P450 Enzymes: Differences between Bacterial and Human Calcitriol Biosynthesis
Year: 2025
Type: article
Abstract: Vitamin D 3 (VD 3 ) is an important natural product with functions in the human body related to bone growth and homeostasis. In the body, vitamin D 3 is converted into the hormone calcitriol by successive activation of the C 25 –H and C 1 –H groups by two cytochrome P450 isozymes that each catalyze a regioselective C–H hydroxylation step. By contrast, in bacteria, both reactions happen in the same P450 isozyme, but the product after the first hydroxylation step does not escape into solution. To understand the differences between human and bacterial VD 3 activation, we performed molecular dynamics and quantum mechanics studies of these enzymes. Molecular dynamics simulations on the four P450 structures for human and bacterial isozymes with VD 3 and 25-hydroxy-VD 3 bound show that the human P450 enzyme for the first hydroxylation step has a small and narrow cavity around the heme, which only fits an aliphatic chain, and hence can only perform C 25 -hydroxylation. On the other hand, the bacterial P450 has a more open and spherical substrate binding pocket where the substrate fits in both orientations. Consequently, 25-hydroxy-VD 3 will bind for a long period of time in the bacterial P450 isozyme that can trigger a second reaction cycle with molecular oxygen. Subsequently, QM calculations on cluster models show that all reaction steps happen through a rate-determining hydrogen atom abstraction. However, the human P450 isozyme reacts with faster kinetics than the bacterial isozyme through better and tighter positioning of the substrate, which highlights the role of the second coordination sphere for enzyme-catalyzed reactions.
DOI: 10.1021/jacs.5c13857
Authors: Yi Zhang, Yuanxin Cao, Sam P. de Visser
Institution: University of Manchester
Language: English
Subfield: Inorganic Chemistry
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W4414564337