Probing Catalytic Residues Responsible for Primer Substrate Reactivity in a Versatile cis -Geranylgeranyl Diphosphate Synthase
- 1Academy of Circular Economy, National Chung Hsing University , , No. 15, Guangming Rd, Neixing Village , ,
- 2National Chiayi University , , No. 300, Xuefu Rd, Luliao Village , East District, ,
- 3National Chung Hsing University , , No. 15, Guangming Rd, Neixing Village , ,
Abstract
Cis-isoprenyl diphosphate synthases (cis-IDSs) catalyze the synthesis of polyisoprenyl diphosphates with varying chain lengths and stereochemistry, yet the molecular mechanism underlying their substrate selectivity remains elusive. Here, we investigated VoDN3985, a cis-IDS from Viburnum odoratissimum, by combining mutagenesis, conditioned molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations. Conditioned MD simulations revealed substrate-dependent differences in geometric preorganization, with geranyl diphosphate (GPP) showing the highest prereactive fraction and farnesyl diphosphate (FPP) sampling more idealized allylic torsional geometries than dimethylallyl diphosphate (DMAPP). Active-site substitutions at Asn64 and His79 expanded primer tolerance to enable DMAPP utilization while preserving concerted substitution pathways in QM/MM profiles. Crucially, selectivity shift from altered configuration-dependent reaction energetics rather than barrier reductions. By decoupling dynamic conformational preorganization from intrinsic reaction-path energetics, this study provides actionable mechanistic principles for rationally engineering cis-IDS substrate selectivity.
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BibTeX
@article{lin2026probing,
title = {{Probing Catalytic Residues Responsible for Primer Substrate Reactivity in a Versatile cis -Geranylgeranyl Diphosphate Synthase}},
author = {Ching-Chih Lin and Miao-Lin Cheng and Tao-Ho Chang and Li-Ting Ma},
journal = {ACS Omega},
year = {2026},
month = oct,
doi = {10.1021/acsomega.6c05022},
url = {https://pubs.acs.org/acsodf/article/doi/10.1021/acsomega.6c05022/5455829/Probing-Catalytic-Residues-Responsible-for-Primer},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Probing Catalytic Residues Responsible for Primer Substrate Reactivity in a Versatile cis -Geranylgeranyl Diphosphate Synthase
AU - Ching-Chih Lin
AU - Miao-Lin Cheng
AU - Tao-Ho Chang
AU - Li-Ting Ma
PY - 2026
DA - 2026/10/22
JO - ACS Omega
DO - 10.1021/acsomega.6c05022
UR - https://pubs.acs.org/acsodf/article/doi/10.1021/acsomega.6c05022/5455829/Probing-Catalytic-Residues-Responsible-for-Primer
AB - Cis-isoprenyl diphosphate synthases (cis-IDSs) catalyze the synthesis of polyisoprenyl diphosphates with varying chain lengths and stereochemistry, yet the molecular mechanism underlying their substrate selectivity remains elusive. Here, we investigated VoDN3985, a cis-IDS from Viburnum odoratissimum, by combining mutagenesis, conditioned molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations. Conditioned MD simulations revealed substrate-dependent differences in geometric preorganization, with geranyl diphosphate (GPP) showing the highest prereactive fraction and farnesyl diphosphate (FPP) sampling more idealized allylic torsional geometries than dimethylallyl diphosphate (DMAPP). Active-site substitutions at Asn64 and His79 expanded primer tolerance to enable DMAPP utilization while preserving concerted substitution pathways in QM/MM profiles. Crucially, selectivity shift from altered configuration-dependent reaction energetics rather than barrier reductions. By decoupling dynamic conformational preorganization from intrinsic reaction-path energetics, this study provides actionable mechanistic principles for rationally engineering cis-IDS substrate selectivity.
SN - 2470-1343
ER -