Jump to main content
Jump to site search
Access to RSC content Close the message box

Continue to access RSC content when you are not at your institution. Follow our step-by-step guide.


Issue 36, 2017, Issue in Progress
Previous Article Next Article

QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme

Author affiliations

Abstract

The type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the reversible isomerization of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Although a growing body of experiments have suggested that the flavin coenzyme of IDI-2 serves a novel function as an acid–base catalyst, the detailed reaction mechanism of IDI-2 is still unknown. In this paper, a combined quantum-mechanical/molecular-mechanical (QM/MM) approach has been applied to investigate the detailed reaction mechanism of IDI-2. The one-base mechanism in which the N-5 nitrogen of the zwitterionic form of reduced FMN acts as the acid–base catalyst has been supported by our computational results, and a IPP-FMN adduct is also proposed for the first time. The mechanistic details including the fundamental reaction pathways, the complete energy profiles of the whole catalytic cycle, and the specific role of the coenzyme and key residues are all obtained. It is proved that IDI-2 employs novel flavin chemistry with the coenzyme acting as a general acid–base catalyst.

Graphical abstract: QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme

Back to tab navigation

Supplementary files

Article information


Submitted
06 Nov 2016
Accepted
13 Apr 2017
First published
21 Apr 2017

This article is Open Access

RSC Adv., 2017,7, 22286-22293
Article type
Paper

QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme

Q. Hou, K. Wang, F. Xu, W. Zhang, K. Ji and Y. Liu, RSC Adv., 2017, 7, 22286
DOI: 10.1039/C6RA26397F

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material and it is not used for commercial purposes.

Reproduced material should be attributed as follows:

  • For reproduction of material from NJC:
    [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
  • For reproduction of material from PCCP:
    [Original citation] - Published by the PCCP Owner Societies.
  • For reproduction of material from PPS:
    [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
  • For reproduction of material from all other RSC journals:
    [Original citation] - Published by The Royal Society of Chemistry.

Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.


Social activity

Search articles by author

Spotlight

Advertisements