Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase—A Computational Study

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.

Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression

“…The systems were first minimized for six rounds, with the positional restraints on the protein backbone gradually decreasing to 100, 75, 50, 25, 10, and 0 kcal/(mol Å 2 ). For each round, the 1200 steepest descent steps followed by 1800 conjugate gradient steps were performed [ 32 ]. After minimization, the system was gradually heated to the target temperature of 300 K under constant pressure periodic boundary conditions (NVT ensemble) for 120 ps with a 1 fs time step.…”

“…For all the MD simulations, the counterions were added to achieve electroneutrality and to satisfy the experimental ionic strength of all the models. The CPPTRAJ utility embedded in the Amber20 program was used to obtain the root mean square deviation (RMSD), root mean square fluctuation (RMSF), average structures, representative structure, and hydrogen bonds from the trajectories [ 32 ].…”

Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis

“…Electron transfer to the Fe(IV) center in 32 and decarboxylation then result in the formation of the first vinyl-substituted intermediate, harderoheme III ( 33 ). The intermediate 33 may be released from and bound again to HemQ in a reoriented conformation for the next round of propionate decarboxylation on ring B. Alternatively, 33 may rotate by 90° in the active site to produce heme b 1 ( 1 ) (Liu et al, 2022 ; Michlits et al, 2020 ; Milazzo et al, 2019 , 2018 ; Sebastiani et al, 2021 ).…”

Structural aspects of enzymes involved in prokaryotic Gram-positive heme biosynthesis

“…When coproheme is bound the catalytic tyrosine is in close proximity to p2 of pyrrole ring A, whereas after the first decarboxylation step MMD rotates in situ and places p4 of pyrrole ring B close to the catalytic tyrosine. [82] , [84] , [85] , [86] , [87] .

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