New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase

Hideaki Unno, Satoshi Yamashita, Yosuke Ikeda, Shin Ya Sekiguchi, Norie Yoshida, Tohru Yoshimura, Masami Kusunoki, Toru Nakayama, Tokuzo Nishino, Hisashi Hemmi

Research output: Contribution to journalArticlepeer-review

41 Citations (Scopus)


Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes.

Original languageEnglish
Pages (from-to)9160-9167
Number of pages8
JournalJournal of Biological Chemistry
Issue number14
Publication statusPublished - 2009 Apr 3

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


Dive into the research topics of 'New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase'. Together they form a unique fingerprint.

Cite this