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de Araújo EA, Cortez AA, Pellegrini VDOA, Vacilotto MM, Cruz AF, Batista PR, Polikarpov I. Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9. Carbohydr Polym 2024; 329:121739. [PMID: 38286536 DOI: 10.1016/j.carbpol.2023.121739] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/31/2024]
Abstract
Carbohydrate-active enzymes from the glycoside hydrolase family 9 (GH9) play a key role in processing lignocellulosic biomass. Although the structural features of some GH9 enzymes are known, the molecular mechanisms that drive their interactions with cellulosic substrates remain unclear. To investigate the molecular mechanisms that the two-domain Bacillus licheniformis BlCel9A enzyme utilizes to depolymerize cellulosic substrates, we used a combination of biochemical assays, X-ray crystallography, small-angle X-ray scattering, and molecular dynamics simulations. The results reveal that BlCel9A breaks down cellulosic substrates, releasing cellobiose and glucose as the major products, but is highly inefficient in cleaving oligosaccharides shorter than cellotetraose. In addition, fungal lytic polysaccharide oxygenase (LPMO) TtLPMO9H enhances depolymerization of crystalline cellulose by BlCel9A, while exhibiting minimal impact on amorphous cellulose. The crystal structures of BlCel9A in both apo form and bound to cellotriose and cellohexaose were elucidated, unveiling the interactions of BlCel9A with the ligands and their contribution to substrate binding and products release. MD simulation analysis reveals that BlCel9A exhibits higher interdomain flexibility under acidic conditions, and SAXS experiments indicate that the enzyme flexibility is induced by pH and/or temperature. Our findings provide new insights into BlCel9A substrate specificity and binding, and synergy with the LPMOs.
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Affiliation(s)
- Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Giuseppe Maximo Scolfaro, 10000, Campinas, SP 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Anelyse Abreu Cortez
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | | | - Milena Moreira Vacilotto
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Amanda Freitas Cruz
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil
| | - Paulo Ricardo Batista
- Oswaldo Cruz Foundation, Scientific Computing Programme, Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Igor Polikarpov
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador Sao Carlense, 400, Sao Carlos, SP 13566-590, Brazil.
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de Oliveira Neto M, de Freitas Fernandes A, Piiadov V, Craievich AF, de Araújo EA, Polikarpov I. SAXSMoW 3.0: New advances in the determination of the molecular weight of proteins in dilute solutions from SAXS intensity data on a relative scale. Protein Sci 2022; 31:251-258. [PMID: 34761467 PMCID: PMC8740845 DOI: 10.1002/pro.4227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023]
Abstract
SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small-angle X-ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.0 determines the linear dependence of the true protein volume on their apparent protein volume, based on SAXS curves calculated for 67,000 protein structures selected from the Protein Data Bank. SAXSMoW 3.0 was tested against 43 experimental SAXS scattering curves from proteins with known molecular weights. Our results demonstrate that most of the molecular weights determined for the nonglycosylated and also for the glycosylated proteins are in good agreement with their expected molecular weights. Additionally, the average discrepancies between the calculated molecular weights and their nominal values for glycosylated proteins are similar to those for nonglycosylated ones.
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Affiliation(s)
- Mario de Oliveira Neto
- Biophysics and Pharmacology DepartmentBioscience Institute, Universidade Estadual PaulistaBotucatuSão PauloBrazil
| | | | - Vassili Piiadov
- Sao Carlos Institute of PhysicsUniversity of Sao PauloSão PauloBrazil
| | | | - Evandro Ares de Araújo
- Brazilian Synchrotron Light LaboratoryBrazilian Center for Research in Energy and MaterialsCampinasSão PauloBrazil
| | - Igor Polikarpov
- Sao Carlos Institute of PhysicsUniversity of Sao PauloSão PauloBrazil
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Leite AET, Briganti L, de Araújo EA, Pellegrini VDOA, Camilo CM, Polikarpov I. Low-resolution molecular shape, biochemical characterization and emulsification properties of a halotolerant esterase from Bacillus licheniformis. Eur Biophys J 2020; 49:435-447. [PMID: 32683479 DOI: 10.1007/s00249-020-01448-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023]
Abstract
Bacterial esterases are highly versatile enzymes, currently widely used in detergents, biosurfactants, bioemulsifiers and as biocatalysts in paper and food industries. Present work describes heterologous expression, purification, and biophysical and biochemical characterization of a halotolerant esterase from Bacillus licheniformis (BlEstA). BlEstA preferentially cleaves pNP-octanoate and both activity and stability of the enzyme increased in the presence of 2 M NaCl, and also with several organic solvents (ethanol, methanol and DMSO). Furthermore, BlEstA has considerable emulsifying properties, particularly with olive oil as substrate. Our studies also show that the enzyme is monomeric in solution and its small-angle X-ray scattering low-resolution molecular envelope fits well its high-resolution homology model.
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Affiliation(s)
- Ana Elisa T Leite
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Lorenzo Briganti
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | | | | | - Cesar Moyses Camilo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil.
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Kadowaki MAS, Higasi PMR, de Godoy MO, de Araújo EA, Godoy AS, Prade RA, Polikarpov I. Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77. Biochim Biophys Acta Gen Subj 2020; 1864:129681. [PMID: 32653619 DOI: 10.1016/j.bbagen.2020.129681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 02/25/2020] [Revised: 06/14/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023]
Abstract
Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H2O2) as by-product. The H2O2 can be provided to lignin degradation pathway, a biotechnological property explored in biofuel production. In the thermophilic fungus Thermothelomyces thermophilus (formerly Myceliophthora thermophila), just one AAOx was identified in the exo-proteome. Methods The glycosylated and non-refolded crystal structure of an AAOx from T. thermophilus at 2.6 Å resolution was elucidated by X-ray crystallography combined with small-angle X-ray scattering (SAXS) studies. Moreover, biochemical analyses were carried out to shed light on enzyme substrate specificity and thermostability. Results This flavoenzyme harbors a flavin adenine dinucleotide as a cofactor and is able to oxidize aromatic substrates and 5-HMF. Our results also show that the enzyme has similar oxidation rates for bulky or simple aromatic substrates such as cinnamyl and veratryl alcohols. Moreover, the crystal structure of MtAAOx reveals an open active site, which might explain observed specificity of the enzyme. Conclusions MtAAOx shows previously undescribed structural differences such as a fully accessible catalytic tunnel, heavy glycosylation and Ca2+ binding site providing evidences for thermostability and activity of the enzymes from AA3_2 subfamily. General significance Structural and biochemical analyses of MtAAOx could be important for comprehension of aryl-alcohol oxidases structure-function relationships and provide additional molecular tools to be used in future biotechnological applications.
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Affiliation(s)
- Marco Antonio Seiki Kadowaki
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
| | - Paula Miwa Rabelo Higasi
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Mariana Ortiz de Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Evandro Ares de Araújo
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Andre Schutzer Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil
| | - Rolf Alexander Prade
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Oklahoma State University, OK, USA
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil.
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Piiadov V, Ares de Araújo E, Oliveira Neto M, Craievich AF, Polikarpov I. SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale. Protein Sci 2018; 28:454-463. [PMID: 30371978 DOI: 10.1002/pro.3528] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [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: 08/02/2018] [Revised: 10/05/2018] [Accepted: 10/08/2018] [Indexed: 11/07/2022]
Abstract
Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.
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Affiliation(s)
- Vassili Piiadov
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Evandro Ares de Araújo
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Mario Oliveira Neto
- Institute of Biosciences, University Estadual Paulista, Botucatu, São Paulo, Brazil
| | | | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
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de Araújo EA, de Oliveira Neto M, Polikarpov I. Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis. Appl Microbiol Biotechnol 2018; 103:1275-1287. [PMID: 30547217 DOI: 10.1007/s00253-018-9508-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/14/2018] [Revised: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Abstract
Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.
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Affiliation(s)
- Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Mário de Oliveira Neto
- Departmento de Física e Biofísica, Universidade Estadual Paulista "Júlio de Mesquita Filho", R. Prof. Dr. Antonio Celso Wagner Zanin 689, Jardim Sao Jose, Botucatu, SP, 18618-970, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil.
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Segato F, Berto GL, Ares de Araújo E, Muniz JR, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-β-1,4-glucanase from glycoside hydrolase family 12. Acta Crystallogr F Struct Biol Commun 2014; 70:267-70. [PMID: 24637772 PMCID: PMC3936441 DOI: 10.1107/s2053230x13034936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 10/13/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Endoglucanases are important enzymes that are involved in the modification and degradation of cellulose. Filamentous fungi such as Aspergillus terreus are effective biomass degraders in nature owing to their capacity to produce an enzymatic arsenal of glycoside hydrolases, including endoglucanase from glycoside hydrolase family 12 (GH12). The A. terreus GH12 endoglucanase was cloned and overexpressed in A. nidulans, purified and crystallized. A single crystal was obtained from a solution consisting of 2 M ammonium sulfate, 5%(v/v) 2-propanol. X-ray diffraction data were collected to a resolution of 1.85 Å using synchrotron radiation and a preliminary molecular-replacement solution was obtained in the trigonal space group P3(2)21. The unit-cell parameters were a = b = 103.24, c = 48.96 Å.
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Affiliation(s)
- Fernando Segato
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Gabriela L. Berto
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - João Renato Muniz
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
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de Araújo EA, Tomazini A, Kadowaki MAS, Murakami MT, Polikarpov I. Crystallization and preliminary X-ray diffraction analysis of a new xyloglucanase from Xanthomonas campestris pv. campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:676-678. [PMID: 23722852 PMCID: PMC3668593 DOI: 10.1107/s174430911301275x] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/02/2013] [Accepted: 05/09/2013] [Indexed: 06/02/2023]
Abstract
Xyloglucanases (Xghs) are important enzymes involved in xyloglucan modification and degradation. Xanthomonas campestris pv. campestris (Xcc) is a phytopathogenic bacterium which produces a large number of glycosyl hydrolases (GH), but has only one family 74 GH (Xcc-Xgh). This enzyme was overexpressed in Escherichia coli, purified and crystallized. Diffraction data sets were collected for the native enzyme and its complex with glucose to maximum resolutions of 2.0 and 2.1 Å, respectively. The data were indexed in a hexagonal crystal system with unit-cell parameters a = b = 153.4, c = 84.9 Å. As indicated by molecular-replacement solution, the crystals belonged to space group P6(1).
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Affiliation(s)
- Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, 400 Trabalhador Saocarlense, 13566-590 São Carlos-SP, Brazil
| | - Atílio Tomazini
- Instituto de Física de São Carlos, Universidade de São Paulo, 400 Trabalhador Saocarlense, 13566-590 São Carlos-SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Instituto de Física de São Carlos, Universidade de São Paulo, 400 Trabalhador Saocarlense, 13566-590 São Carlos-SP, Brazil
| | - Mário Tyago Murakami
- Laboratório Nacional de Biociências, CNPEM, 10000 Giuseppe Máximo Scolfaro, 13083-100, Campinas-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, 400 Trabalhador Saocarlense, 13566-590 São Carlos-SP, Brazil
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