1
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Wang L, Wang YY, Chen ZL, Li YH. Enzymatic characterization and thermostability improvement of an acidophilic endoxylanase PphXyn11 from Paenibacillus physcomitrellae XB. Protein Expr Purif 2024; 219:106482. [PMID: 38583789 DOI: 10.1016/j.pep.2024.106482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
GH11 enzyme is known to be specific and efficient for the hydrolysis of xylan. It has been isolated from many microorganisms, and its enzymatic characteristics and thermostability vary between species. In this study, a GH11 enzyme PphXyn11 from a novel xylan-degrading strain of Paenibacillus physcomitrellae XB was characterized, and five mutants were constructed to try to improve the enzyme's thermostability. The results showed that PphXyn11 was an acidophilic endo-β-1,4-xylanase with the optimal reaction pH of 3.0-4.0, and it could deconstruct different kinds of xylan substrates efficiently, such as beechwood xylan, wheat arabinoxylan and xylo-oligosaccharides, to produce xylobiose and xylotriose as the main products at the optimal reaction temperature of 40 °C. Improvement of the thermal stability of PphXyn11 using site-directed mutagenesis revealed that three mutants, W33C/N47C, S127C/N174C and S49E, designed by adding the disulfide bonds at the N-terminal, C-terminal and increasing the charged residues on the surface of PphXyn11 respectively, could increase the enzymatic activity and thermal stablility significantly and make the optimal reaction temperature reach 50 °C. Molecular dynamics simulations as well as computed the numbers of salt bridges and hydrogen bonds indicated that the protein structures of these three mutants were more stable than the wild type, which provided theoretical support for their improved thermal stability. Certainly, further research is necessary to improve the enzymatic characteristics of PphXyn11 to achieve the bioconversion of hemicellulosic biomass on an applicable scale.
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Affiliation(s)
- Le Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Yan Wang
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Zhi Ling Chen
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Yan Hong Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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2
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MacDonald ME, Wells NGM, Hassan BA, Dudley JA, Walters KJ, Korzhnev DM, Aramini JM, Smith CA. Effects of Xylanase A double mutation on substrate specificity and structural dynamics. J Struct Biol 2024; 216:108082. [PMID: 38438058 DOI: 10.1016/j.jsb.2024.108082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
While protein activity is traditionally studied with a major focus on the active site, the activity of enzymes has been hypothesized to be linked to the flexibility of adjacent regions, warranting more exploration into how the dynamics in these regions affects catalytic turnover. One such enzyme is Xylanase A (XylA), which cleaves hemicellulose xylan polymers by hydrolysis at internal β-1,4-xylosidic linkages. It contains a "thumb" region whose flexibility has been suggested to affect the activity. The double mutation D11F/R122D was previously found to affect activity and potentially bias the thumb region to a more open conformation. We find that the D11F/R122D double mutation shows substrate-dependent effects, increasing activity on the non-native substrate ONPX2 but decreasing activity on its native xylan substrate. To characterize how the double mutant causes these kinetics changes, nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations were used to probe structural and flexibility changes. NMR chemical shift perturbations revealed structural changes in the double mutant relative to the wild-type, specifically in the thumb and fingers regions. Increased slow-timescale dynamics in the fingers region was observed as intermediate-exchange line broadening. Lipari-Szabo order parameters show negligible changes in flexibility in the thumb region in the presence of the double mutation. To help understand if there is increased energetic accessibility to the open state upon mutation, alchemical free energy simulations were employed that indicated thumb opening is more favorable in the double mutant. These studies aid in further characterizing how flexibility in adjacent regions affects the function of XylA.
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Affiliation(s)
- Meagan E MacDonald
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States; Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Bakar A Hassan
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Joshua A Dudley
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, United States
| | - James M Aramini
- Structural Biology Initiative, Advanced Science Research Center, The City University of New York, New York, NY 10031, United States
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, United States.
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3
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Molina GA, Mendes LFS, Fuzo CA, Costa-Filho AJ, Ward RJ. Mapping secondary substrate-binding sites on the GH11 xylanase from Bacillus subtilis. FEBS Lett 2024; 598:363-376. [PMID: 38253842 DOI: 10.1002/1873-3468.14799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Xylanases are of significant interest for biomass conversion technologies. Here, we investigated the allosteric regulation of xylan hydrolysis by the Bacillus subtilis GH11 endoxylanase. Molecular dynamics simulations (MDS) in the presence of xylobiose identified binding to the active site and two potential secondary binding sites (SBS) around surface residues Asn54 and Asn151. Arabinoxylan titration experiments with single cysteine mutants N54C and N151C labeled with the thiol-reactive fluorophore acrylodan or the ESR spin-label MTSSL validated the MDS results. Ligand binding at the SBS around Asn54 confirms previous reports, and analysis of the second SBS around N151C discovered in the present study includes residues Val98/Ala192/Ser155/His156. Understanding the regulation of xylanases contributes to efforts for industrial decarbonization and to establishing a sustainable energy matrix.
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Affiliation(s)
- Gustavo Avelar Molina
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis Felipe Santos Mendes
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos Alessandro Fuzo
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonio José Costa-Filho
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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4
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Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021; 22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
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Affiliation(s)
- Jelena Vucinic
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Gleb Novikov
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Correspondence:
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5
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Marneth K, van den Elst H, Cramer‐Blok A, Codee J, Overkleeft HS, Aerts JMFG, Ubbink M, Ben Bdira F. Tuning the Transglycosylation Reaction of a GH11 Xylanase by a Delicate Enhancement of its Thumb Flexibility. Chembiochem 2021; 22:1743-1749. [PMID: 33534182 PMCID: PMC8251542 DOI: 10.1002/cbic.202000856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Glycoside hydrolases (GHs) are attractive tools for multiple biotechnological applications. In conjunction with their hydrolytic function, GHs can perform transglycosylation under specific conditions. In nature, oligosaccharide synthesis is performed by glycosyltransferases (GTs); however, the industrial use of GTs is limited by their instability in solution. A key difference between GTs and GHs is the flexibility of their binding site architecture. We have used the xylanase from Bacillus circulans (BCX) to study the interplay between active-site flexibility and transglycosylation. Residues of the BCX "thumb" were substituted to increase the flexibility of the enzyme binding site. Replacement of the highly conserved residue P116 with glycine shifted the balance of the BCX enzymatic reaction toward transglycosylation. The effects of this point mutation on the structure and dynamics of BCX were investigated by NMR spectroscopy. The P116G mutation induces subtle changes in the configuration of the thumb and enhances the millisecond dynamics of the active site. Based on our findings, we propose the remodelling of the GH enzymes glycon site flexibility as a strategy to improve the transglycosylation efficiency of these biotechnologically important catalysts.
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Affiliation(s)
- Kim Marneth
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hans van den Elst
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Anneloes Cramer‐Blok
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen Codee
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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6
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Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Phys Chem Chem Phys 2020; 22:25936-25948. [PMID: 33164009 DOI: 10.1039/d0cp04415f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The worldwide dependence of population on fossil fuels continues to have several harmful implications for the environment. Bioethanol is an excellent option for renewable fuel to replace the current greenhouse gas emitters. In addition, its production by enzymatic route has gained space among the industrial processes because it replaces the traditional acid treatment. Due to its high versatility, the xylanase family is used in this process as an accessory enzyme for degrading the lignocellulosic substrate of biomass. A chimera built by a xylanolytic domain (Xyl) and a xylose-binding protein (XBP) showed an experimentally improved catalytic efficiency and interdomain allosteric modulation after xylose binding. In this context, we performed a quantum biochemistry characterization of the interactions between these domains and dynamic cross-correlation (DCC) analysis after performing molecular dynamics (DM) simulations of the systems in the presence and absence of xylose in the XBP active site. We used the density functional theory (DFT) within the molecular fractionation with the conjugated caps (MFCC) approach to describe the pair energies, and the corresponding energy difference between the chimera domains responsible for the allosteric effect and amino acid DCC to evaluate the interdomain coupling differences between the energy states. The detailed energetic investigation together with the related structural and dynamics counterparts revealed the molecular mechanisms of chimeric improvement of the xylanase activity observed experimentally. This mechanism was correlated with greater stability and high connectivity at the interdomain interface in the xylose bound relative to the free chimera. We identify the contributions of hydrogen bonds, hydrophobic interactions and water-mediated interactions in the interdomain region responsible for stability together with the structural and dynamical elements related to the allosteric effect. Taken together, these observations led to a comprehensive understanding of the chimera's modulatory action that occurs through the formation of a highly connected interface that makes the essential movements related to xylanolytic activity in xylanase correlated to those of the xylose-binding protein.
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7
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Greener approach for pulp and paper industry by Xylanase and Laccase. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101604] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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8
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Interaction of drugs amlodipine and paroxetine with the metabolizing enzyme CYP2B4: a molecular dynamics simulation study. J Mol Model 2018; 24:67. [DOI: 10.1007/s00894-018-3617-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/08/2018] [Indexed: 12/26/2022]
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9
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Ventorim RZ, de Oliveira Mendes TA, Trevizano LM, dos Santos Camargos AM, Guimarães VM. Impact of the removal of N-terminal non-structured amino acids on activity and stability of xylanases from Orpinomyces sp. PC-2. Int J Biol Macromol 2018; 106:312-319. [DOI: 10.1016/j.ijbiomac.2017.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/19/2017] [Accepted: 08/01/2017] [Indexed: 11/17/2022]
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10
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Silva SB, Pinheiro MP, Fuzo CA, Silva SR, Ferreira TL, Lourenzoni MR, Nonato MC, Vieira DS, Ward RJ. The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. Int J Biol Macromol 2017; 97:574-584. [DOI: 10.1016/j.ijbiomac.2017.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
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11
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Childers MC, Daggett V. Insights from molecular dynamics simulations for computational protein design. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2017; 2:9-33. [PMID: 28239489 PMCID: PMC5321087 DOI: 10.1039/c6me00083e] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.
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Affiliation(s)
| | - Valerie Daggett
- Corresponding author: , Phone: 1.206.685.7420, Fax: 1.206.685.3300
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12
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Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry 2016; 55:4184-96. [PMID: 27387012 DOI: 10.1021/acs.biochem.6b00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Nhung Nguyen-Thi
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - David N Bernard
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , 320 East Superior Street, Chicago, Illinois 60611, United States
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
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13
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Thermostabilization of Bacillus subtilis GH11 xylanase by surface charge engineering. Int J Biol Macromol 2016; 87:522-8. [DOI: 10.1016/j.ijbiomac.2016.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 11/24/2022]
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14
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Ribeiro LF, Tullman J, Nicholes N, Silva SRB, Vieira DS, Ostermeier M, Ward RJ. A xylose-stimulated xylanase-xylose binding protein chimera created by random nonhomologous recombination. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:119. [PMID: 27274356 PMCID: PMC4896006 DOI: 10.1186/s13068-016-0529-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Saccharification of lignocellulosic material by xylanases and other glycoside hydrolases is generally conducted at high concentrations of the final reaction products, which frequently inhibit the enzymes used in the saccharification process. Using a random nonhomologous recombination strategy, we have fused the GH11 xylanase from Bacillus subtilis (XynA) with the xylose binding protein from Escherichia coli (XBP) to produce an enzyme that is allosterically stimulated by xylose. RESULTS The pT7T3GFP_XBP plasmid containing the XBP coding sequence was randomly linearized with DNase I, and ligated with the XynA coding sequence to create a random XynA-XBP insertion library, which was used to transform E. coli strain JW3538-1 lacking the XBP gene. Screening for active XBP was based on the expression of GFP from the pT7T3GFP_XBP plasmid under the control of a xylose inducible promoter. In the presence of xylose, cells harboring a functional XBP domain in the fusion protein (XBP+) showed increased GFP fluorescence and were selected using FACS. The XBP+ cells were further screened for xylanase activity by halo formation around xylanase producing colonies (XynA+) on LB-agar-xylan media after staining with Congo red. The xylanase activity ratio with xylose/without xylose in supernatants from the XBP+/XynA+ clones was measured against remazol brilliant blue xylan. A clone showing an activity ratio higher than 1.3 was selected where the XynA was inserted after the asparagine 271 in the XBP, and this chimera was denominated as XynA-XBP271. The XynA-XBP271 was more stable than XynA at 55 °C, and in the presence of xylose the catalytic efficiency was ~3-fold greater than the parental xylanase. Molecular dynamics simulations predicted the formation of an extended protein-protein interface with coupled movements between the XynA and XBP domains. In the XynA-XBP271 with xylose bound to the XBP domain, the mobility of a β-loop in the XynA domain results in an increased access to the active site, and may explain the observed allosteric activation. CONCLUSIONS The approach presented here provides an important advance for the engineering enzymes that are stimulated by the final product.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- />Johns Hopkins University, Baltimore, MD USA
- />Departamento de Bioquímica e Imunologia, FMRP-Universidade de São Paulo-USP, Ribeirão Preto, SP Brazil
| | - Jennifer Tullman
- />Johns Hopkins University, Baltimore, MD USA
- />Institute for Bioscience and Biotechnology Research, Rockville, MD USA
| | | | | | | | | | - Richard John Ward
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol-CTBE, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- />Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP 14040-901 Brazil
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Rapid asymmetric reduction of ethyl 4-chloro-3-oxobutanoate using a thermostabilized mutant of ketoreductase ChKRED20. Appl Microbiol Biotechnol 2015; 100:3567-75. [DOI: 10.1007/s00253-015-7200-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/19/2015] [Accepted: 11/24/2015] [Indexed: 11/25/2022]
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18
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Jaeger VW, Pfaendtner J. Structure, dynamics, and activity of xylanase solvated in binary mixtures of ionic liquid and water. ACS Chem Biol 2013; 8:1179-86. [PMID: 23517495 DOI: 10.1021/cb3006837] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have discovered that a family 11 xylanase from Trichoderma longibrachiatum maintains significant activity in low concentrations of the ionic liquids (IL) 1-ethyl-3-methyl-imidazolium acetate ([EMIM][OAc]) or 1-ethyl-3-methyl-imidazolium ethyl sulfate ([EMIM][EtSO4]) in water. In order to understand the mechanisms by which the ionic liquids affect the activity of xylanase, we conducted molecular dynamics simulations of the enzyme in various concentrations of the cosolvent. The simulations show that higher concentrations of ionic liquid correlate with less deviation from the starting crystallographic structure. Dynamic motion of the protein is severely dampened by even the lowest tested concentrations of ionic liquid as measured by root-mean-square fluctuation. Principal component analysis shows that the characteristics of the main modes of enzyme motion are greatly affected by the choice of solvent. Cations become kinetically trapped in the binding pocket, allowing them to act as a competitive inhibitor to the natural substrate. Dynamic light scattering and kinetic studies evaluated the stability of the enzyme in the new solvents. These studies indicate that likely factors in the loss of enzyme activity for this xylanase are the dampening of dynamic motion and kinetic trapping of cations in the binding pocket as opposed to the denaturing of the protein.
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Affiliation(s)
- Vance W. Jaeger
- Department of Chemical
Engineering, University of Washington,
Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical
Engineering, University of Washington,
Seattle, Washington 98195, United States
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19
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Singh RK, Tiwari MK, Kim D, Kang YC, Ramachandran P, Lee JK. Molecular cloning and characterization of a GH11 endoxylanase from Chaetomium globosum, and its use in enzymatic pretreatment of biomass. Appl Microbiol Biotechnol 2012. [PMID: 23184220 DOI: 10.1007/s00253-012-4577-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An endo-1,4-β-xylanase gene, xylcg, was cloned from Chaetomium globosum and successfully expressed in Escherichia coli. The complete gene of 675 bp was amplified, cloned into the pET 28(a) vector, and expressed. The optimal conditions for the highest activity of the purified recombinant XylCg were observed at a temperature of 40 °C and pH of 5.5. Using oat-spelt xylan, the determined K m, V max, and k cat/K m values were 0.243 mg ml⁻¹, 4,530 U mg⁻¹ protein, and 7,640 ml s⁻¹ mg⁻¹, respectively. A homology model and sequence analysis of XylCg, along with the biochemical properties, confirmed that XylCg belongs to the GH11 family. Rice straw pretreated with XylCg showed 30 % higher conversion yield than the rice straw pretreated with a commercial xylanase. Although xylanases have been characterized from fungal and bacterial sources, C. globosum XylCg is distinguished from other xylanases by its high catalytic efficiency and its effectiveness in the pretreatment of lignocellulosic biomass.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, South Korea
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20
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Pan D, Xue W, Zhang W, Liu H, Yao X. Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study. Biochim Biophys Acta Gen Subj 2012; 1820:1526-34. [DOI: 10.1016/j.bbagen.2012.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 06/03/2012] [Accepted: 06/04/2012] [Indexed: 12/19/2022]
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21
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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22
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Paës G, Cortés J, Siméon T, O'Donohue MJ, Tran V. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. Comput Struct Biotechnol J 2012; 1:e201207001. [PMID: 24688637 PMCID: PMC3962102 DOI: 10.5936/csbj.201207001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/23/2012] [Accepted: 05/27/2012] [Indexed: 12/17/2022] Open
Abstract
Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis.
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Affiliation(s)
- Gabriel Paës
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France
| | - Juan Cortés
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Thierry Siméon
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Michael J O'Donohue
- INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; INRA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France ; INSA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France
| | - Vinh Tran
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France
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23
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Song L, Siguier B, Dumon C, Bozonnet S, O'Donohue MJ. Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:3. [PMID: 22244361 PMCID: PMC3299623 DOI: 10.1186/1754-6834-5-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/13/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND Improving the hydrolytic performance of hemicellulases on lignocellulosic biomass is of considerable importance for second-generation biorefining. To address this problem, and also to gain greater understanding of structure-function relationships, especially related to xylanase action on complex biomass, we have implemented a combinatorial strategy to engineer the GH11 xylanase from Thermobacillus xylanilyticus (Tx-Xyn). RESULTS Following in vitro enzyme evolution and screening on wheat straw, nine best-performing clones were identified, which display mutations at positions 3, 6, 27 and 111. All of these mutants showed increased hydrolytic activity on wheat straw, and solubilized arabinoxylans that were not modified by the parental enzyme. The most active mutants, S27T and Y111T, increased the solubilization of arabinoxylans from depleted wheat straw 2.3-fold and 2.1-fold, respectively, in comparison to the wild-type enzyme. In addition, five mutants, S27T, Y111H, Y111S, Y111T and S27T-Y111H increased total hemicellulose conversion of intact wheat straw from 16.7%tot. xyl (wild-type Tx-Xyn) to 18.6% to 20.4%tot. xyl. Also, all five mutant enzymes exhibited a better ability to act in synergy with a cellulase cocktail (Accellerase 1500), thus procuring increases in overall wheat straw hydrolysis. CONCLUSIONS Analysis of the results allows us to hypothesize that the increased hydrolytic ability of the mutants is linked to (i) improved ligand binding in a putative secondary binding site, (ii) the diminution of surface hydrophobicity, and/or (iii) the modification of thumb flexibility, induced by mutations at position 111. Nevertheless, the relatively modest improvements that were observed also underline the fact that enzyme engineering alone cannot overcome the limits imposed by the complex organization of the plant cell wall and the lignin barrier.
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Affiliation(s)
- Letian Song
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Béatrice Siguier
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- CNRS, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
| | - Claire Dumon
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Sophie Bozonnet
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Michael J O'Donohue
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
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24
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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25
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Vieira DS, Ward RJ. Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis. J Mol Model 2011; 18:1473-9. [PMID: 21785938 DOI: 10.1007/s00894-011-1172-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/29/2011] [Indexed: 11/29/2022]
Abstract
Xylanases (EC 3.2.1.8 endo-1,4-glycosyl hydrolase) catalyze the hydrolysis of xylan, an abundant hemicellulose of plant cell walls. Access to the catalytic site of GH11 xylanases is regulated by movement of a short β-hairpin, the so-called thumb region, which can adopt open or closed conformations. A crystallographic study has shown that the D11F/R122D mutant of the GH11 xylanase A from Bacillus subtilis (BsXA) displays a stable "open" conformation, and here we report a molecular dynamics simulation study comparing this mutant with the native enzyme over a range of temperatures. The mutant open conformation was stable at 300 and 328 K, however it showed a transition to the closed state at 338 K. Analysis of dihedral angles identified thumb region residues Y113 and T123 as key hinge points which determine the open-closed transition at 338 K. Although the D11F/R122D mutations result in a reduction in local inter-intramolecular hydrogen bonding, the global energies of the open and closed conformations in the native enzyme are equivalent, suggesting that the two conformations are equally accessible. These results indicate that the thumb region shows a broader degree of energetically permissible conformations which regulate the access to the active site region. The R122D mutation contributes to the stability of the open conformation, but is not essential for thumb dynamics, i.e., the wild type enzyme can also adapt to the open conformation.
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Affiliation(s)
- Davi Serradella Vieira
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Avenida dos Bandeirantes, 3900 - 14040-90 Ribeirão Preto, SP, Brazil.
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26
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Morin A, Kaufmann KW, Fortenberry C, Harp JM, Mizoue LS, Meiler J. Computational design of an endo-1,4-beta-xylanase ligand binding site. Protein Eng Des Sel 2011; 24:503-16. [PMID: 21349882 DOI: 10.1093/protein/gzr006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-β-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterization of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 β-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the β-xylanase proteins.
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Affiliation(s)
- Andrew Morin
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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