Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase

Autores
Briganti, Lorenzo; Capetti, Caio; Pellegrini, Vanessa O. A.; Ghio, Silvina; Campos, Eleonora; Nascimento, Alessandro S.; Polikarpov, Igor
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.
Instituto de Biotecnología
Fil: Briganti, Lorenzo. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Capetti, Caio. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Pellegrini, Vanessa O. A. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Ghio, Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Campos, Eleonora. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nascimento, Alessandro S. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Polikarpov, Igor. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fuente
Computational and Structural Biotechnology Journal 19 : 1557-1566 (Marzo 2021)
Materia
Paenibacillus
Enzimas
Cristalización
Biología Molecular
Bioinformática
Enzymes
Crystallization
Molecular Biology
Bioinformatics
Structural Analysis
Análisis Estructural
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/11740

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oai_identifier_str oai:localhost:20.500.12123/11740
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanaseBriganti, LorenzoCapetti, CaioPellegrini, Vanessa O. A.Ghio, SilvinaCampos, EleonoraNascimento, Alessandro S.Polikarpov, IgorPaenibacillusEnzimasCristalizaciónBiología MolecularBioinformáticaEnzymesCrystallizationMolecular BiologyBioinformaticsStructural AnalysisAnálisis EstructuralGlycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.Instituto de BiotecnologíaFil: Briganti, Lorenzo. Universidade de São Paulo. Instituto de Física de São Carlos; BrasilFil: Capetti, Caio. Universidade de São Paulo. Instituto de Física de São Carlos; BrasilFil: Pellegrini, Vanessa O. A. Universidade de São Paulo. Instituto de Física de São Carlos; BrasilFil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Ghio, Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Campos, Eleonora. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nascimento, Alessandro S. Universidade de São Paulo. Instituto de Física de São Carlos; BrasilFil: Polikarpov, Igor. Universidade de São Paulo. Instituto de Física de São Carlos; BrasilElsevier2022-04-27T14:25:30Z2022-04-27T14:25:30Z2021-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/11740https://www.sciencedirect.com/science/article/pii/S200103702100074X2001-0370https://doi.org/10.1016/j.csbj.2021.03.002Computational and Structural Biotechnology Journal 19 : 1557-1566 (Marzo 2021)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:30:40Zoai:localhost:20.500.12123/11740instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:30:43.236INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
title Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
spellingShingle Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
Briganti, Lorenzo
Paenibacillus
Enzimas
Cristalización
Biología Molecular
Bioinformática
Enzymes
Crystallization
Molecular Biology
Bioinformatics
Structural Analysis
Análisis Estructural
title_short Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
title_full Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
title_fullStr Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
title_full_unstemmed Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
title_sort Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
dc.creator.none.fl_str_mv Briganti, Lorenzo
Capetti, Caio
Pellegrini, Vanessa O. A.
Ghio, Silvina
Campos, Eleonora
Nascimento, Alessandro S.
Polikarpov, Igor
author Briganti, Lorenzo
author_facet Briganti, Lorenzo
Capetti, Caio
Pellegrini, Vanessa O. A.
Ghio, Silvina
Campos, Eleonora
Nascimento, Alessandro S.
Polikarpov, Igor
author_role author
author2 Capetti, Caio
Pellegrini, Vanessa O. A.
Ghio, Silvina
Campos, Eleonora
Nascimento, Alessandro S.
Polikarpov, Igor
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Paenibacillus
Enzimas
Cristalización
Biología Molecular
Bioinformática
Enzymes
Crystallization
Molecular Biology
Bioinformatics
Structural Analysis
Análisis Estructural
topic Paenibacillus
Enzimas
Cristalización
Biología Molecular
Bioinformática
Enzymes
Crystallization
Molecular Biology
Bioinformatics
Structural Analysis
Análisis Estructural
dc.description.none.fl_txt_mv Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.
Instituto de Biotecnología
Fil: Briganti, Lorenzo. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Capetti, Caio. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Pellegrini, Vanessa O. A. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Ghio, Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Campos, Eleonora. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nascimento, Alessandro S. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
Fil: Polikarpov, Igor. Universidade de São Paulo. Instituto de Física de São Carlos; Brasil
description Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.
publishDate 2021
dc.date.none.fl_str_mv 2021-03
2022-04-27T14:25:30Z
2022-04-27T14:25:30Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/11740
https://www.sciencedirect.com/science/article/pii/S200103702100074X
2001-0370
https://doi.org/10.1016/j.csbj.2021.03.002
url http://hdl.handle.net/20.500.12123/11740
https://www.sciencedirect.com/science/article/pii/S200103702100074X
https://doi.org/10.1016/j.csbj.2021.03.002
identifier_str_mv 2001-0370
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv Computational and Structural Biotechnology Journal 19 : 1557-1566 (Marzo 2021)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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