An enzymatic atavist revealed in dual pathways for water activation.

Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinc...

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Autores principales: Donghong Min, Helen R Josephine, Hongzhi Li, Clemens Lakner, Iain S MacPherson, Gavin J P Naylor, David Swofford, Lizbeth Hedstrom, Wei Yang
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Publicado: Public Library of Science (PLoS) 2008
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Acceso en línea:https://doaj.org/article/ddb9bd56b4474bdcb042295fdd6460ad
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spelling oai:doaj.org-article:ddb9bd56b4474bdcb042295fdd6460ad2021-11-25T05:33:58ZAn enzymatic atavist revealed in dual pathways for water activation.1544-91731545-788510.1371/journal.pbio.0060206https://doaj.org/article/ddb9bd56b4474bdcb042295fdd6460ad2008-08-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18752347/pdf/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a "Wang-Landau" metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme.Donghong MinHelen R JosephineHongzhi LiClemens LaknerIain S MacPhersonGavin J P NaylorDavid SwoffordLizbeth HedstromWei YangPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 6, Iss 8, p e206 (2008)
institution DOAJ
collection DOAJ
language EN
topic Biology (General)
QH301-705.5
spellingShingle Biology (General)
QH301-705.5
Donghong Min
Helen R Josephine
Hongzhi Li
Clemens Lakner
Iain S MacPherson
Gavin J P Naylor
David Swofford
Lizbeth Hedstrom
Wei Yang
An enzymatic atavist revealed in dual pathways for water activation.
description Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a "Wang-Landau" metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme.
format article
author Donghong Min
Helen R Josephine
Hongzhi Li
Clemens Lakner
Iain S MacPherson
Gavin J P Naylor
David Swofford
Lizbeth Hedstrom
Wei Yang
author_facet Donghong Min
Helen R Josephine
Hongzhi Li
Clemens Lakner
Iain S MacPherson
Gavin J P Naylor
David Swofford
Lizbeth Hedstrom
Wei Yang
author_sort Donghong Min
title An enzymatic atavist revealed in dual pathways for water activation.
title_short An enzymatic atavist revealed in dual pathways for water activation.
title_full An enzymatic atavist revealed in dual pathways for water activation.
title_fullStr An enzymatic atavist revealed in dual pathways for water activation.
title_full_unstemmed An enzymatic atavist revealed in dual pathways for water activation.
title_sort enzymatic atavist revealed in dual pathways for water activation.
publisher Public Library of Science (PLoS)
publishDate 2008
url https://doaj.org/article/ddb9bd56b4474bdcb042295fdd6460ad
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