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dc.contributor.author
Briganti, Lorenzo
dc.contributor.author
Capetti, Caio
dc.contributor.author
Pellegrini, Vanessa O. A.
dc.contributor.author
Ghio, Silvina
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dc.contributor.author
Campos, Eleonora
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dc.contributor.author
Nascimento, Alessandro S.
dc.contributor.author
Polikarpov, Igor
dc.date.available
2022-11-02T05:08:59Z
dc.date.issued
2021-01
dc.identifier.citation
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
dc.identifier.uri
http://hdl.handle.net/11336/175899
dc.description.abstract
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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Elsevier
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.subject
CRYSTALLOGRAPHIC STRUCTURE
dc.subject
GH11 XYLANASE
dc.subject
GLYCOSYL HYDROLASE
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MOLECULAR DYNAMICS
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PAENIBACILLUS SP
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SECONDARY BINDING SITE
dc.subject.classification
Bioproductos, Biomateriales, Bioplásticos, Biocombustibles, Bioderivados, etc.
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dc.subject.classification
Biotecnología Industrial
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dc.subject.classification
INGENIERÍAS Y TECNOLOGÍAS
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dc.title
Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2022-03-09T17:58:58Z
dc.identifier.eissn
2001-0370
dc.journal.volume
19
dc.journal.pagination
1557-1566
dc.journal.pais
Países Bajos
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dc.journal.ciudad
Amsterdam
dc.description.fil
Fil: Briganti, Lorenzo. Universidade de Sao Paulo; Brasil
dc.description.fil
Fil: Capetti, Caio. Universidade de Sao Paulo; Brasil
dc.description.fil
Fil: Pellegrini, Vanessa O. A.. Universidade de Sao Paulo; Brasil
dc.description.fil
Fil: Ghio, Silvina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina
dc.description.fil
Fil: Campos, Eleonora. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Nascimento, Alessandro S.. Universidade de Sao Paulo; Brasil
dc.description.fil
Fil: Polikarpov, Igor. Universidade de Sao Paulo; Brasil
dc.journal.title
Computational and Structural Biotechnology Journal
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S200103702100074X
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1016/j.csbj.2021.03.002
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