Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors

Scientific Reports
Vivek S BharadwajMichael F Crowley

Abstract

Biological routes to the production of fuels from renewable feedstocks hold significant promise in our efforts towards a sustainable future. The fatty acid decarboxylase enzyme (OleTJE) is a cytochrome P450 enzyme that converts long and medium chain fatty acids to terminal alkenes and shares significant similarities in terms of structure, substrate scope and mechanism with the hydroxylase cytochrome P450 (P450BSβ). Recent reports have demonstrated that catalytic pathways in these enzymes bifurcate when the heme is in its iron-hydroxo (compound II) state. In spite of significant similarities, the fundamental underpinnings of their different characteristic wild-type reactivities remain ambiguous. Here, we develop point charges, modified parameters and report molecular simulations of this crucial intermediate step. Water occupancies and substrate mobility at the active site are observed to be vital differentiating aspects between the two enzymes in the compound II state and corroborate recent experimental hypotheses. Apart from increased substrate mobility in the hydroxylase, which could have implications for enabling the rebound mechanism for hydroxylation, OleTJE is characterized by much stronger binding of the substrate carboxy...Continue Reading

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Citations

May 26, 2020·Chemistry : a European Journal·Julia ArmbrusterAlexander Dennig
Dec 18, 2020·Biophysical Journal·Matthew D McCoyM Saleet Jafri
Oct 14, 2020·Inorganic Chemistry·Daniel C CumminsDavid P Goldberg

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Software Mentioned

CAVER
GAFF
house VMD script
pK
ptraj
OleT
Gaussian
MMPBSA
OleT JE
antechamber

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