PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 28577910-3 2017 Over the past decade, a variety of biochemical, spectroscopic, structural and mechanistic studies of IDI-2 have provided mounting evidence that the flavin coenzyme of IDI-2 acts in a most unusual manner - as an acid/base catalyst to mediate a 1,3-proton addition/elimination reaction. 4,6-dinitro-o-cresol 148-154 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 101-106 28577910-3 2017 Over the past decade, a variety of biochemical, spectroscopic, structural and mechanistic studies of IDI-2 have provided mounting evidence that the flavin coenzyme of IDI-2 acts in a most unusual manner - as an acid/base catalyst to mediate a 1,3-proton addition/elimination reaction. 4,6-dinitro-o-cresol 148-154 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 167-172 28577910-4 2017 While not entirely without precedent, IDI-2 is by far the most extensively studied flavoenzyme that employs flavin-mediated acid/base catalysis. 4,6-dinitro-o-cresol 108-114 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 38-43 28577910-5 2017 Thus, IDI-2 serves as an important mechanistic model for understanding this often overlooked, but potentially widespread reactivity of flavin coenzymes. 4,6-dinitro-o-cresol 135-141 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 6-11 27003727-4 2016 For IDI-2 from the pathogenic bacterium Streptococcus pneumoniae, the flavin can be treated kinetically as a dissociable cosubstrate in incubations with IPP and excess NADH. 4,6-dinitro-o-cresol 70-76 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 4-9 27003727-10 2016 Dithionite reduction of FMN in the IDI-2 FMN and IPP mixture was biphasic with k(red)(IDI-2 FMN IPP (fast)) = 326 s(-1) and k(red)(IDI-2 FMN IPP (slow)) = 6.9 s(-1) The pseudo-first-order rate constant for the slow component was similar to those for NADH reduction of the flavin in the IDI-2 FMN and IPP mixture and may reflect a rate-limiting conformational change in the enzyme. 4,6-dinitro-o-cresol 272-278 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 35-40 20593767-6 2010 Linear free energy relationships (LFERs) between the electronic properties of the flavin and the steady state kinetic parameters of the IDI-2 catalyzed reaction were observed. 4,6-dinitro-o-cresol 82-88 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 136-141 20593767-8 2010 Cumulatively, the data presented in this work (and in other studies) suggest that the reduced FMN coenzyme of IDI-2 functions as an acid/base catalyst, with the N5 atom of the flavin likely playing a critical role in the deprotonation of IPP en route to DMAPP formation. 4,6-dinitro-o-cresol 176-182 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 110-115 18345677-3 2008 Type I IPP isomerase (IDI-1) utilizes a divalent metal in a protonation-deprotonation reaction; whereas, the type II enzyme (IDI-2) requires reduced flavin. 4,6-dinitro-o-cresol 149-155 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 125-130 18345677-11 2008 These studies indicate that the irreversible inhibitors inactivate the reduced flavin required for catalysis by electrophilic alkylation and are consistent with a protonation-deprotonation mechanism for the isomerization catalyzed by IDI-2. 4,6-dinitro-o-cresol 79-85 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 234-239 17580897-4 2007 In particular, the catalytic mechanisms of two of these enzymes, UGM and IDI-2, may involve novel flavin chemistry. 4,6-dinitro-o-cresol 98-104 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 73-78 22158896-3 2011 Both the crystal structures of IDI-2 binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5, which had been proposed previously. 4,6-dinitro-o-cresol 49-55 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 31-36 22158896-3 2011 Both the crystal structures of IDI-2 binding the flavin-inhibitor adduct and the UV-visible spectra of the adducts indicate that the covalent bond is formed at C4a of flavin rather than at N5, which had been proposed previously. 4,6-dinitro-o-cresol 167-173 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 31-36 22158896-4 2011 In addition, the high-resolution crystal structures of IDI-2-substrate complexes and the kinetic studies of new mutants confirmed that only the flavin cofactor can catalyze protonation of the substrates and suggest that N5 of flavin is most likely to be involved in proton transfer. 4,6-dinitro-o-cresol 144-150 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 55-60 22158896-4 2011 In addition, the high-resolution crystal structures of IDI-2-substrate complexes and the kinetic studies of new mutants confirmed that only the flavin cofactor can catalyze protonation of the substrates and suggest that N5 of flavin is most likely to be involved in proton transfer. 4,6-dinitro-o-cresol 226-232 isopentenyl-diphosphate delta isomerase 2 Homo sapiens 55-60