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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/11740
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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 |
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INTA Digital (INTA) |
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INTA Digital (INTA) |
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Instituto Nacional de Tecnología Agropecuaria |
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INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria |
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tripaldi.nicolas@inta.gob.ar |
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