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.
Fil: Briganti, Lorenzo. Universidade de Sao Paulo; Brasil
Fil: Capetti, Caio. Universidade de Sao Paulo; Brasil
Fil: Pellegrini, Vanessa O. A.. Universidade de Sao Paulo; Brasil
Fil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nascimento, Alessandro S.. Universidade de Sao Paulo; Brasil
Fil: Polikarpov, Igor. Universidade de Sao Paulo; Brasil
Materia
CRYSTALLOGRAPHIC STRUCTURE
GH11 XYLANASE
GLYCOSYL HYDROLASE
MOLECULAR DYNAMICS
PAENIBACILLUS SP
SECONDARY BINDING SITE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/175899
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/175899
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
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, IgorCRYSTALLOGRAPHIC STRUCTUREGH11 XYLANASEGLYCOSYL HYDROLASEMOLECULAR DYNAMICSPAENIBACILLUS SPSECONDARY BINDING SITEhttps://purl.org/becyt/ford/2.9https://purl.org/becyt/ford/2Glycoside 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.Fil: Briganti, Lorenzo. Universidade de Sao Paulo; BrasilFil: Capetti, Caio. Universidade de Sao Paulo; BrasilFil: Pellegrini, Vanessa O. A.. Universidade de Sao Paulo; BrasilFil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; ArgentinaFil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nascimento, Alessandro S.. Universidade de Sao Paulo; BrasilFil: Polikarpov, Igor. Universidade de Sao Paulo; BrasilElsevier2021-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/175899Briganti, Lorenzo; Capetti, Caio; Pellegrini, Vanessa O. A.; Ghio, Silvina; Campos, Eleonora; et al.; Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase; Elsevier; Computational and Structural Biotechnology Journal; 19; 1-2021; 1557-15662001-0370CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S200103702100074Xinfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.csbj.2021.03.002info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:22:44Zoai:ri.conicet.gov.ar:11336/175899instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-10 13:22:44.83CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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
CRYSTALLOGRAPHIC STRUCTURE
GH11 XYLANASE
GLYCOSYL HYDROLASE
MOLECULAR DYNAMICS
PAENIBACILLUS SP
SECONDARY BINDING SITE
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 CRYSTALLOGRAPHIC STRUCTURE
GH11 XYLANASE
GLYCOSYL HYDROLASE
MOLECULAR DYNAMICS
PAENIBACILLUS SP
SECONDARY BINDING SITE
topic CRYSTALLOGRAPHIC STRUCTURE
GH11 XYLANASE
GLYCOSYL HYDROLASE
MOLECULAR DYNAMICS
PAENIBACILLUS SP
SECONDARY BINDING SITE
purl_subject.fl_str_mv https://purl.org/becyt/ford/2.9
https://purl.org/becyt/ford/2
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.
Fil: Briganti, Lorenzo. Universidade de Sao Paulo; Brasil
Fil: Capetti, Caio. Universidade de Sao Paulo; Brasil
Fil: Pellegrini, Vanessa O. A.. Universidade de Sao Paulo; Brasil
Fil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
Fil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nascimento, Alessandro S.. Universidade de Sao Paulo; Brasil
Fil: Polikarpov, Igor. Universidade de Sao Paulo; 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 2021-01
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/11336/175899
Briganti, Lorenzo; Capetti, Caio; Pellegrini, Vanessa O. A.; Ghio, Silvina; Campos, Eleonora; et al.; Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase; Elsevier; Computational and Structural Biotechnology Journal; 19; 1-2021; 1557-1566
2001-0370
CONICET Digital
CONICET
url http://hdl.handle.net/11336/175899
identifier_str_mv Briganti, Lorenzo; Capetti, Caio; Pellegrini, Vanessa O. A.; Ghio, Silvina; Campos, Eleonora; et al.; Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase; Elsevier; Computational and Structural Biotechnology Journal; 19; 1-2021; 1557-1566
2001-0370
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S200103702100074X
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.csbj.2021.03.002
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.48226

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