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de Morais MAB, Polo CC, Domingues MN, Persinoti GF, Pirolla RAS, de Souza FHM, Correa JBDL, dos Santos CR, Murakami MT. Exploring the Molecular Basis for Substrate Affinity and Structural Stability in Bacterial GH39 β-Xylosidases. Front Bioeng Biotechnol 2020; 8:419. [PMID: 32500063 PMCID: PMC7242879 DOI: 10.3389/fbioe.2020.00419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
The glycoside hydrolase family 39 (GH39) is a functionally expanding family with limited understanding about the molecular basis for substrate specificity and extremophilicity. In this work, we demonstrate the key role of the positive-subsite region in modulating substrate affinity and how the lack of a C-terminal extension impacts on oligomerization and structural stability of some GH39 members. The crystallographic and SAXS structures of a new GH39 member from the phytopathogen Xanthomonas citri support the importance of an extended C-terminal to promote oligomerization as a molecular strategy to enhance thermal stability. Comparative structural analysis along with site-directed mutagenesis showed that two residues located at the positive-subsite region, Lys166 and Asp167, are critical to substrate affinity and catalytic performance, by inducing local changes in the active site for substrate binding. These findings expand the molecular understanding of the mechanisms involved in substrate recognition and structural stability of the GH39 family, which might be instrumental for biological insights, rational enzyme engineering and utilization in biorefineries.
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Affiliation(s)
| | - Carla Cristina Polo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Mariane Noronha Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | | | | | | - Camila Ramos dos Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Mário Tyago Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
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Zanphorlin LM, de Morais MAB, Diogo JA, Domingues MN, de Souza FHM, Ruller R, Murakami MT. Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43. Biotechnol Bioeng 2019; 116:734-744. [PMID: 30556897 DOI: 10.1002/bit.26899] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/01/2018] [Accepted: 12/14/2018] [Indexed: 11/07/2022]
Abstract
Rational design is an important tool for sculpting functional and stability properties of proteins and its potential can be much magnified when combined with in vitro and natural evolutionary diversity. Herein, we report the structure-guided design of a xylose-releasing exo-β-1,4-xylanase from an inactive member of glycoside hydrolase family 43 (GH43). Structural analysis revealed a nonconserved substitution (Lys247 ) that results in the disruption of the hydrogen bond network that supports catalysis. The mutation of this residue to a conserved serine restored the catalytic activity and crystal structure elucidation of the mutant confirmed the recovery of the proper orientation of the catalytically relevant histidine. Interestingly, the tailored enzyme can cleave both xylooligosaccharides and xylan, releasing xylose as the main product, being the first xylose-releasing exo-β-1,4-xylanase reported in the GH43 family. This enzyme presents a unique active-site topology when compared with closely related β-xylosidases, which is the absence of a hydrophobic barrier at the positive-subsite region, allowing the accommodation of long substrates. Therefore, the combination of rational design for catalytic activation along with naturally occurring differences in the substrate binding interface led to the discovery of a novel activity within the GH43 family. In addition, these results demonstrate the importance of solvation of the β-propeller hollow for GH43 catalytic function and expand our mechanistic understanding about the diverse modes of action of GH43 members, a key and polyspecific carbohydrate-active enzyme family abundant in most plant cell-wall-degrading microorganisms.
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Affiliation(s)
- Letícia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mariana Abrahão Bueno de Morais
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - José Alberto Diogo
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mariane Noronha Domingues
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Flávio Henrique Moreira de Souza
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Roberto Ruller
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
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dos Santos CR, de Giuseppe PO, de Souza FHM, Zanphorlin LM, Domingues MN, Pirolla RAS, Honorato RV, Tonoli CCC, de Morais MAB, de Matos Martins VP, Fonseca LM, Büchli F, de Oliveira PSL, Gozzo FC, Murakami MT. The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. Biotechnol Biofuels 2018; 11:223. [PMID: 30127853 PMCID: PMC6087011 DOI: 10.1186/s13068-018-1212-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Arabinoxylan is an abundant polysaccharide in industrially relevant biomasses such as sugarcane, corn stover and grasses. However, the arabinofuranosyl di-substitutions that decorate the xylan backbone are recalcitrant to most known arabinofuranosidases (Abfs). RESULTS In this work, we identified a novel GH51 Abf (XacAbf51) that forms trimers in solution and can cope efficiently with both mono- and di-substitutions at terminal or internal xylopyranosyl units of arabinoxylan. Using mass spectrometry, the kinetic parameters of the hydrolysis of 33-α-l-arabinofuranosyl-xylotetraose and 23,33-di-α-l-arabinofuranosyl-xylotetraose by XacAbf51 were determined, demonstrating the capacity of this enzyme to cleave arabinofuranosyl linkages of internal mono- and di-substituted xylopyranosyl units. Complementation studies of fungal enzyme cocktails with XacAbf51 revealed an increase of up to 20% in the release of reducing sugars from pretreated sugarcane bagasse, showing the biotechnological potential of a generalist GH51 in biomass saccharification. To elucidate the structural basis for the recognition of internal di-substitutions, the crystal structure of XacAbf51 was determined unveiling the existence of a pocket strategically arranged near to the - 1 subsite that can accommodate a second arabinofuranosyl decoration, a feature not described for any other GH51 Abf structurally characterized so far. CONCLUSIONS In summary, this study reports the first kinetic characterization of internal di-substitution release by a GH51 Abf, provides the structural basis for this activity and reveals a promising candidate for industrial processes involving plant cell wall depolymerization.
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Affiliation(s)
- Camila Ramos dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Flávio Henrique Moreira de Souza
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Letícia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariane Noronha Domingues
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Renan Augusto Siqueira Pirolla
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Rodrigo Vargas Honorato
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariana Abrahão Bueno de Morais
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Vanesa Peixoto de Matos Martins
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Lucas Miranda Fonseca
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fernanda Büchli
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fábio Cesar Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, Sao Paulo 13083-861 Brazil
| | - Mário Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
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