Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase-A Computational Study.

Wei Liu,Guangju Chen,Hongwei Tan,Yutian Song,Xichen Li,Yunjie Pang

doi:10.3390/ijms23052564

Wei Liu, Guangju Chen + Show 4 more

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https://doi.org/10.3390/ijms23052564

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Abstract

Coproheme decarboxylase (ChdC) is an important enzyme in the coproporphyrin-dependent pathway (CPD) of Gram-positive bacteria that decarboxylates coproheme on two propionates at position 2 and position 4 sequentially to generate heme b by using H2O2 as an oxidant. This work focused on the ChdC from Geobacillus stearothermophilus (GsChdC) to elucidate the mechanism of its sequential two-step decarboxylation of coproheme. The models of GsChdC in a complex with substrate and reaction intermediate were built to investigate the reorienting mechanism of harderoheme. Targeted molecular dynamics simulations on these models validated that harderoheme is able to rotate in the active site of GsChdC with a 19.06-kcal·mol−1 energy barrier after the first step of decarboxylation to bring the propionate at position 4 in proximity of Tyr145 to continue the second decarboxylation step. The harderoheme rotation mechanism is confirmed to be much easier than the release–rebinding mechanism. In the active site of GsChdC, Trp157 and Trp198 comprise a “gate” construction to regulate the clockwise rotation of the harderoheme. Lys149 plays a critical role in the rotation mechanism, which not only keeps the Trp157–Trp198 “gate” from being closed but also guides the propionate at position 4 through the gap between Trp157 and Trp198 through a salt bridge interaction.

Highlights

As the most ubiquitous member of the metalloporphyrin family, heme b is present in various proteins such as hemoglobin, myoglobin, peroxidases, cytochrome P450, NO synthase and mitochondrial complexes II and III [1–3]
coproporphyrin-dependent pathway (CPD) pathways share a common process in the final stage to decarboxylate coproheme into heme b by employing H2 O2 as the oxidant, in which coproheme is decarboxylated on two propionates at position 2 and position 4 sequentially by coproheme decarboxylase (ChdC) [10–14]
By analyzing the targeted molecular dynamics (TMD) trajectory, we found that the anticlockwise rotation is barely blocked by the Trp157

Summary

Introduction

As the most ubiquitous member of the metalloporphyrin family, heme b is present in various proteins such as hemoglobin, myoglobin, peroxidases, cytochrome P450, NO synthase and mitochondrial complexes II and III [1–3]. There is more than one pathway for heme b biosynthesis, including the protoporphyrin-dependent pathway (PPD) in Gram-negative bacteria and the coproporphyrin-dependent pathway (CPD) in Gram-positive bacteria [8,9]. Both the PPD and CPD pathways share a common process in the final stage to decarboxylate coproheme into heme b by employing H2 O2 as the oxidant, in which coproheme is decarboxylated on two propionates at position 2 and position 4 sequentially by coproheme decarboxylase (ChdC) [10–14]. More than 20 different available crystal structures of ChdCs from different bacteria have been deposited in the Protein Data Bank (www.pdb.org, 1 November 2021) [17]. In 2017, DuBois and coworkers solved the crystal structure of ChdC from

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