Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1371/journal.pone.0196918 http://hdl.handle.net/11449/164219 |
Resumo: | Organic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (C-p) toward hydroperoxides. In the closed state, the thiolate of C-p is in close proximity to the guanidinium group of Arg19. Ohr enzymes can also assume an open state, where the loop containing the catalytic Arg is far away from C-p and Glu51. Here, we aimed to gain insights into the putative structural switches of the Ohr catalytic cycle. First, we describe the crystal structure of Ohr from Xylella fastidiosa (XfOhr) in the open state that, together with the previously described XfOhr structure in the closed state, may represent two snapshots along the coordinate of the enzyme-catalyzed reaction. These two structures were used for the experimental validation of molecular dynamics (MD) simulations. MD simulations employing distinct protonation states and in silico mutagenesis indicated that the polar interactions of Arg19 with Glu51 and C-p contributed to the stabilization of XfOhr in the closed state. Indeed, C-p oxidation to the disulfide state facilitated the switching of the Arg19 loop from the closed to the open state. In addition to the Arg19 loop, other portions of XfOhr displayed high mobility, such as a loop rich in Gly residues. In summary, we obtained a high correlation between crystallographic data, MD simulations and biochemical/enzymatic assays. The dynamics of the Ohr enzymes are unique among the Cys-based peroxidases, in which the active site Arg undergoes structural switches throughout the catalytic cycle, while C-p remains relatively static. |
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Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approachesOrganic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (C-p) toward hydroperoxides. In the closed state, the thiolate of C-p is in close proximity to the guanidinium group of Arg19. Ohr enzymes can also assume an open state, where the loop containing the catalytic Arg is far away from C-p and Glu51. Here, we aimed to gain insights into the putative structural switches of the Ohr catalytic cycle. First, we describe the crystal structure of Ohr from Xylella fastidiosa (XfOhr) in the open state that, together with the previously described XfOhr structure in the closed state, may represent two snapshots along the coordinate of the enzyme-catalyzed reaction. These two structures were used for the experimental validation of molecular dynamics (MD) simulations. MD simulations employing distinct protonation states and in silico mutagenesis indicated that the polar interactions of Arg19 with Glu51 and C-p contributed to the stabilization of XfOhr in the closed state. Indeed, C-p oxidation to the disulfide state facilitated the switching of the Arg19 loop from the closed to the open state. In addition to the Arg19 loop, other portions of XfOhr displayed high mobility, such as a loop rich in Gly residues. In summary, we obtained a high correlation between crystallographic data, MD simulations and biochemical/enzymatic assays. The dynamics of the Ohr enzymes are unique among the Cys-based peroxidases, in which the active site Arg undergoes structural switches throughout the catalytic cycle, while C-p remains relatively static.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Redox Processes in BiomedicineUniv Sao Paulo, Inst Quim, Dept Quim Fundamental, Sao Paulo, SP, BrazilUniv Sao Paulo, Inst Biociencias, Dept Genet & Biol Evolut, Sao Paulo, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Campus Litoral Paulista, Sao Vicente, SP, BrazilUniv Fed Sao Paulo, Dept Bioquim, Sao Paulo, SP, BrazilUniv Estadual Paulista, Inst Biociencias, Campus Litoral Paulista, Sao Vicente, SP, BrazilRedox Processes in Biomedicine: 13/07937-8FAPESP: 2008/07971-3FAPESP: 2009/12885-1FAPESP: 2005/50056-6FAPESP: 2014/01614-5FAPESP: 2012/06633-2FAPESP: 2016/12392-9Public Library ScienceUniversidade de São Paulo (USP)Universidade Estadual Paulista (Unesp)Universidade Federal de São Paulo (UNIFESP)Piccirillo, ErikaAlegria, Thiago G. P.Discola, Karen F.Cussiol, Jose A. R. R.Domingos, Renato M.Oliveira, Marcos A. de [UNESP]Rezende, Leandro deNetto, Luis E. S.Amaral, Antonia T-do2018-11-26T17:51:44Z2018-11-26T17:51:44Z2018-05-21info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article23application/pdfhttp://dx.doi.org/10.1371/journal.pone.0196918Plos One. San Francisco: Public Library Science, v. 13, n. 5, 23 p., 2018.1932-6203http://hdl.handle.net/11449/16421910.1371/journal.pone.0196918WOS:000432537100011WOS000432537100011.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPlos One1,164info:eu-repo/semantics/openAccess2023-10-01T06:08:20Zoai:repositorio.unesp.br:11449/164219Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-10-01T06:08:20Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
title |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
spellingShingle |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches Piccirillo, Erika |
title_short |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
title_full |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
title_fullStr |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
title_full_unstemmed |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
title_sort |
Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches |
author |
Piccirillo, Erika |
author_facet |
Piccirillo, Erika Alegria, Thiago G. P. Discola, Karen F. Cussiol, Jose A. R. R. Domingos, Renato M. Oliveira, Marcos A. de [UNESP] Rezende, Leandro de Netto, Luis E. S. Amaral, Antonia T-do |
author_role |
author |
author2 |
Alegria, Thiago G. P. Discola, Karen F. Cussiol, Jose A. R. R. Domingos, Renato M. Oliveira, Marcos A. de [UNESP] Rezende, Leandro de Netto, Luis E. S. Amaral, Antonia T-do |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Estadual Paulista (Unesp) Universidade Federal de São Paulo (UNIFESP) |
dc.contributor.author.fl_str_mv |
Piccirillo, Erika Alegria, Thiago G. P. Discola, Karen F. Cussiol, Jose A. R. R. Domingos, Renato M. Oliveira, Marcos A. de [UNESP] Rezende, Leandro de Netto, Luis E. S. Amaral, Antonia T-do |
description |
Organic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (C-p) toward hydroperoxides. In the closed state, the thiolate of C-p is in close proximity to the guanidinium group of Arg19. Ohr enzymes can also assume an open state, where the loop containing the catalytic Arg is far away from C-p and Glu51. Here, we aimed to gain insights into the putative structural switches of the Ohr catalytic cycle. First, we describe the crystal structure of Ohr from Xylella fastidiosa (XfOhr) in the open state that, together with the previously described XfOhr structure in the closed state, may represent two snapshots along the coordinate of the enzyme-catalyzed reaction. These two structures were used for the experimental validation of molecular dynamics (MD) simulations. MD simulations employing distinct protonation states and in silico mutagenesis indicated that the polar interactions of Arg19 with Glu51 and C-p contributed to the stabilization of XfOhr in the closed state. Indeed, C-p oxidation to the disulfide state facilitated the switching of the Arg19 loop from the closed to the open state. In addition to the Arg19 loop, other portions of XfOhr displayed high mobility, such as a loop rich in Gly residues. In summary, we obtained a high correlation between crystallographic data, MD simulations and biochemical/enzymatic assays. The dynamics of the Ohr enzymes are unique among the Cys-based peroxidases, in which the active site Arg undergoes structural switches throughout the catalytic cycle, while C-p remains relatively static. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:51:44Z 2018-11-26T17:51:44Z 2018-05-21 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1371/journal.pone.0196918 Plos One. San Francisco: Public Library Science, v. 13, n. 5, 23 p., 2018. 1932-6203 http://hdl.handle.net/11449/164219 10.1371/journal.pone.0196918 WOS:000432537100011 WOS000432537100011.pdf |
url |
http://dx.doi.org/10.1371/journal.pone.0196918 http://hdl.handle.net/11449/164219 |
identifier_str_mv |
Plos One. San Francisco: Public Library Science, v. 13, n. 5, 23 p., 2018. 1932-6203 10.1371/journal.pone.0196918 WOS:000432537100011 WOS000432537100011.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Plos One 1,164 |
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info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
23 application/pdf |
dc.publisher.none.fl_str_mv |
Public Library Science |
publisher.none.fl_str_mv |
Public Library Science |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
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Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
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UNESP |
reponame_str |
Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1799964394927423488 |