Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase
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 hyd...
| Autores principales: | , , , , , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2022
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| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855036628308852736 |
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| author | Briganti, Lorenzo Capetti, Caio Pellegrini, Vanessa O. A. Ghio, Silvina Campos, Eleonora Nascimento, Alessandro S. Polikarpov, Igor |
| author_browse | Briganti, Lorenzo Campos, Eleonora Capetti, Caio Ghio, Silvina Nascimento, Alessandro S. Pellegrini, Vanessa O. A. Polikarpov, Igor |
| author_facet | Briganti, Lorenzo Capetti, Caio Pellegrini, Vanessa O. A. Ghio, Silvina Campos, Eleonora Nascimento, Alessandro S. Polikarpov, Igor |
| author_sort | Briganti, Lorenzo |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA11740 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | INTA117402022-04-27T14:30:24Z Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase Briganti, Lorenzo Capetti, Caio Pellegrini, Vanessa O. A. Ghio, Silvina Campos, Eleonora Nascimento, Alessandro S. Polikarpov, Igor Paenibacillus Enzimas Cristalización Biología Molecular Bioinformática Enzymes Crystallization Molecular Biology Bioinformatics Structural Analysis Análisis Estructural 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 2022-04-27T14:25:30Z 2022-04-27T14:25:30Z 2021-03 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf Elsevier Computational and Structural Biotechnology Journal 19 : 1557-1566 (Marzo 2021) |
| spellingShingle | Paenibacillus Enzimas Cristalización Biología Molecular Bioinformática Enzymes Crystallization Molecular Biology Bioinformatics Structural Analysis Análisis Estructural Briganti, Lorenzo Capetti, Caio Pellegrini, Vanessa O. A. Ghio, Silvina Campos, Eleonora Nascimento, Alessandro S. Polikarpov, Igor 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 |
| 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_short | 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 |
| topic | Paenibacillus Enzimas Cristalización Biología Molecular Bioinformática Enzymes Crystallization Molecular Biology Bioinformatics Structural Analysis Análisis Estructural |
| 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 |
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