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Nin-Hill A, Ardevol A, Biarnés X, Planas A, Rovira C. Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase. Chemistry 2023; 29:e202302555. [PMID: 37804517 DOI: 10.1002/chem.202302555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
Bacterial β-glycosidases are hydrolytic enzymes that depolymerize polysaccharides such as β-cellulose, β-glucans and β-xylans from different sources, offering diverse biomedical and industrial uses. It has been shown that a conformational change of the substrate, from a relaxed 4 C1 conformation to a distorted 1 S3 /1,4 B conformation of the reactive sugar, is necessary for catalysis. However, the molecular determinants that stabilize the substrate's distortion are poorly understood. Here we use quantum mechanics/molecular mechanics (QM/MM)-based molecular dynamics methods to assess the impact of the interaction between the reactive sugar, i. e. the one at subsite -1, and the catalytic nucleophile (a glutamate) on substrate conformation. We show that the hydrogen bond involving the C2 exocyclic group and the nucleophile controls substrate conformation: its presence preserves sugar distortion, whereas its absence (e.g. in an enzyme mutant) knocks it out. We also show that 2-deoxy-2-fluoro derivatives, widely used to trap the reaction intermediates by X-ray crystallography, reproduce the conformation of the hydrolysable substrate at the experimental conditions. These results highlight the importance of the 2-OH⋅⋅⋅nucleophile interaction in substrate recognition and catalysis in endo-glycosidases and can inform mutational campaigns aimed to search for more efficient enzymes.
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Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
- present address: Toulouse Biotechnology Institute, TBI, Universite de Toulouse, CNRS, INRAE, INSA Toulouse, 135, avenue de Rangueil, 31077, Toulouse Cedex 04, France
| | - Albert Ardevol
- CSIRO Manufacturing, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) &, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
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2
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Cuxart I, Coines J, Esquivias O, Faijes M, Planas A, Biarnés X, Rovira C. Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto- N-biosidase. ACS Catal 2022; 12:4737-4743. [PMID: 35465242 PMCID: PMC9016705 DOI: 10.1021/acscatal.2c00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/26/2022] [Indexed: 12/22/2022]
Abstract
![]()
Bifidobacterium
bifidum lacto-N-biosidase (LnbB)
is a critical enzyme for the degradation
of human milk oligosaccharides in the gut microbiota of breast-fed
infants. Guided by recent crystal structures, we unveil its molecular
mechanism of catalysis using QM/MM metadynamics. We show that the
oligosaccharide substrate follows 1S3/1,4B → [4E]‡ → 4C1/4H5 and 4C1/4H5 → [4E/4H5]‡ → 1,4B conformational itineraries for the two
successive reaction steps, with reaction free energy barriers in agreement
with experiments. The simulations also identify a critical histidine
(His263) that switches between two orientations to modulate the pKa of the acid/base residue, facilitating catalysis.
The reaction intermediate of LnbB is best depicted as an oxazolinium
ion, with a minor population of neutral oxazoline. The present study
sheds light on the processing of oligosaccharides of the early life
microbiota and will be useful for the engineering of LnbB and similar
glycosidases for biocatalysis.
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Affiliation(s)
- Irene Cuxart
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Oriol Esquivias
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08020 Barcelona, Spain
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3
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Zhang S, Chen KY, Zou X. Carbohydrate-Protein Interactions: Advances and Challenges. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2021; 21:147-163. [PMID: 34366717 DOI: 10.4310/cis.2021.v21.n1.a7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A carbohydrate, also called saccharide in biochemistry, is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. For example, sugars are low molecular-weight carbohydrates, and starches are high molecular-weight carbohydrates. Carbohydrates are the most abundant organic substances in nature and essential constituents of all living things. Protein-carbohydrate interactions play important roles in many biological processes, such as cell growth, differentiation, and aggregation. They also have broad applications in pharmaceutical drug design. In this review, we will summarize the characteristic features of protein-carbohydrate interactions and review the computational methods for structure prediction, energy calculations, and kinetic studies of protein-carbohydrate complexes. Finally, we will discuss the challenges in this field.
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Affiliation(s)
- Shuang Zhang
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Kyle Yu Chen
- Rock Bridge High School, 4303 South Providence Rd, Columbia, MO 65203, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
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4
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Madayi D, P H S, K K E. A Glucose binding lectin from Leucaena leucocephala seeds and its mitogenic activity against human lymphocytes. Int J Biol Macromol 2020; 163:431-441. [PMID: 32645492 DOI: 10.1016/j.ijbiomac.2020.07.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 06/29/2020] [Accepted: 07/04/2020] [Indexed: 11/25/2022]
Abstract
Lectins are a specialized group of proteins with immense biological properties and applications. This study describes the purification and characterization of a lectin from Leucaena leucocephala seeds, a plant belonging to the Fabaceae family. Leucaena leucocephala lectin (LLL) was purified by a two-step purification method involving DEAE-cellulose anion exchange chromatography and Sephadex G-75 size exclusion chromatography. The isolated lectin displayed a high haemagglutination titre upon treatment with rabbit erythrocytes. SDS-PAGE and Reverse-Phase High performance liquid chromatography (RP-HPLC) analysis experimentally revealed the presence of three bands corresponding to 37, 27 and 20 kDa indicating the presence of isolectins. Periodic Acid Schiff's (PAS) staining of LLL confirmed the presence of glycoprotein. Various biochemical parameters were analysed to study its effect on the haemagglutination activity. Sugar inhibition studies experimentally revealed that Glucose was the most potent inhibitor. Fluorescence spectrometric analysis of LLL and Glucose indicated a strong interaction with an association constant of 0.159 × 103 M-1. Circular Dichroism spectroscopy indicated a higher alpha helical content (25.27%). LLL was observed to possess mitogenic activity against Peripheral blood mononuclear cells (PBMC). The present investigation reports the isolation of a novel lectin from this plant which could contribute towards the diagnostic studies of certain diseases and for its therapeutic potential.
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Affiliation(s)
- Deepti Madayi
- Department of Biotechnology, University of Calicut, Kerala 673635, India.
| | - Surya P H
- Department of Biotechnology, University of Calicut, Kerala 673635, India
| | - Elyas K K
- Department of Biotechnology, University of Calicut, Kerala 673635, India.
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5
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Diwan D, Shinkai K, Tetsuka T, Cao B, Arai H, Koyama T, Hatano K, Matsuoka K. Synthetic Assembly of Mannose Moieties Using Polymer Chemistry and the Biological Evaluation of Its Interaction towards Concanavalin A. Molecules 2017; 22:E157. [PMID: 28106805 PMCID: PMC6155820 DOI: 10.3390/molecules22010157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022] Open
Abstract
Protein-carbohydrate interactions exhibit myriad intracellular recognition events, so understanding and investigating their specific interaction with high selectivity and strength are of crucial importance. In order to examine the effect of multivalent binding on the specificity of protein-carbohydrate interactions, we synthesized mannose glycosides as a novel type of glycosylated monomer and glycopolymers of polyacrylamide derivatives with α-mannose (α-Man) by radical polymerization and monitored their strength of interaction with concanavalin A (Con A) by surface plasmon resonance (SPR) detection. In a quantitative test using the Con A-immobilized sensor surface, the kinetic affinity for the synthesized polymers, 8a (KD = 3.3 × 10-6 M) and 8b (KD = 5.3 × 10-5 M), were concentration-dependent, showing strong, specific molecular recognition abilities with lectin. Our study showed the enhancement in recognition specificity for multivalent saccharides, which is often mediated by cell surface carbohydrate-binding proteins that exhibit weak affinity and broad specificity for the individual ligands.
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Affiliation(s)
- Deepti Diwan
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Kohei Shinkai
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Toshihiro Tetsuka
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Bin Cao
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Hidenao Arai
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Tetsuo Koyama
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Ken Hatano
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
| | - Koji Matsuoka
- Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
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6
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Substrate-Binding Site of Family 11 Xylanase fromBacillus firmusK-1 by Molecular Docking. Biosci Biotechnol Biochem 2014; 73:833-9. [DOI: 10.1271/bbb.80731] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Lucas R, Peñalver P, Gómez-Pinto I, Vengut-Climent E, Mtashobya L, Cousin J, Maldonado OS, Perez V, Reynes V, Aviñó A, Eritja R, González C, Linclau B, Morales JC. Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water. J Org Chem 2014; 79:2419-29. [PMID: 24552250 DOI: 10.1021/jo402700y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.
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Affiliation(s)
- Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla , 49 Américo Vespucio, 41092, Sevilla, Spain
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8
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del Carmen Fernández-Alonso M, Díaz D, Berbis MÁ, Marcelo F, Cañada J, Jiménez-Barbero J. Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design. Curr Protein Pept Sci 2013; 13:816-30. [PMID: 23305367 PMCID: PMC3706953 DOI: 10.2174/138920312804871175] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 02/04/2023]
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.
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9
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Biarnés X, Ardèvol A, Iglesias-Fernández J, Planas A, Rovira C. Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State. J Am Chem Soc 2011; 133:20301-9. [DOI: 10.1021/ja207113e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Carme Rovira
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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10
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Functional analyses of multiple lichenin-degrading enzymes from the rumen bacterium Ruminococcus albus 8. Appl Environ Microbiol 2011; 77:7541-50. [PMID: 21890664 DOI: 10.1128/aem.06088-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ruminococcus albus 8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence of R. albus revealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived from R. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber.
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11
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Addington T, Calisto B, Alfonso-Prieto M, Rovira C, Fita I, Planas A. Re-engineering specificity in 1,3-1, 4-β-glucanase to accept branched xyloglucan substrates. Proteins 2010; 79:365-75. [DOI: 10.1002/prot.22884] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Planas A, Nieto J, Abel M, Segade A. Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism ofBacillus1,3-1,4-β-glucanase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001618500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Biarnés X, Ardèvol A, Planas A, Rovira C. Substrate conformational changes in glycoside hydrolase catalysis. A first-principles molecular dynamics study. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420903408252] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Morales JC, Reina JJ, Díaz I, Aviñó A, Nieto PM, Eritja R. Experimental measurement of carbohydrate-aromatic stacking in water by using a dangling-ended DNA model system. Chemistry 2008; 14:7828-35. [PMID: 18637649 DOI: 10.1002/chem.200800335] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-carbohydrate recognition is of fundamental importance for a large number of biological processes; carbohydrate-aromatic stacking is a widespread, but poorly understood, structural motif in this recognition. We describe, for the first time, the measurement of carbohydrate-aromatic interactions from their contribution to the stability of a dangling-ended DNA model system. We observe clear differences in the energetics of the interactions of several monosaccharides with a benzene moiety depending on the number of hydroxy groups, the stereochemistry, and the presence of a methyl group in the pyranose ring. A fucose-benzene pair is the most stabilizing of the studied series (-0.4 Kcal mol(-1)) and this interaction can be placed in the same range as other more studied interactions with aromatic residues of proteins, such as Phe-Phe, Phe-Met, or Phe-His. The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction.
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Affiliation(s)
- Juan C Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla, Spain.
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15
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Eneyskaya EV, Ivanen DR, Bobrov KS, Isaeva-Ivanova LS, Shabalin KA, Savel'ev AN, Golubev AM, Kulminskaya AA. Biochemical and kinetic analysis of the GH3 family β-xylosidase from Aspergillus awamori X-100. Arch Biochem Biophys 2007; 457:225-34. [PMID: 17145041 DOI: 10.1016/j.abb.2006.10.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 10/20/2006] [Accepted: 10/22/2006] [Indexed: 11/30/2022]
Abstract
The beta-xylosidase from Aspergillus awamori X-100 belonging to the family 3 glycoside hydrolase revealed a distinctive transglycosylating ability to produce xylooligosaccharides with degree of polymerization more than 7. In order to explain this fact, the enzyme has been subjected to the detailed biochemical study. The enzymatic hydrolysis of p-nitrophenyl beta-D-xylopyranoside was found to occur with overall retention of substrate anomeric configuration suggesting cleavage of xylosidic bonds through a double-displacement mechanism. Kinetic study with aryl beta-xylopyranosides substrates, in which leaving group pK(a)s were in the range of 3.96-10.32, revealed monotonic function of log(k(cat)) and no correlation of log(k(cat)/Km) versus pKa values indicating deglycosylation as a rate-limiting step for the enzymatic hydrolysis. The classical bell-shaped pH dependence of k(cat)/Km indicated two ionizable groups in the beta-xylosidase active site with apparent pKa values of 2.2 and 6.4. The kinetic parameters of hydrolysis, Km and k(cat), of p-nitrophenyl beta-D-1,4-xylooligosaccharides were very close to those for hydrolysis of p-nitrophenyl-beta-D-xylopyranoside. Increase of p-nitrophenyl-beta-D-xylopyranoside concentration up to 80 mM led to increasing of the reaction velocity resulting in k(cat)(app)=81 s(-1). Addition of alpha-methyl D-xylopyranoside to the reaction mixture at high concentration of p-nitrophenyl-beta-D-xylopyranoside (50 mM) caused an acceleration of the beta-xylosidase-catalyzed reactions and appearance of a new transglycosylation product, alpha-methyl D-xylopyranosyl-1,4-beta-D-xylopyranoside, that was identified by 1H NMR spectroscopy. The kinetic model suggested for the enzymatic reaction was consistent with the results obtained.
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Affiliation(s)
- Elena V Eneyskaya
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biology Division, Gatchina 188300, Russia
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16
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Gaiser OJ, Piotukh K, Ponnuswamy MN, Planas A, Borriss R, Heinemann U. Structural basis for the substrate specificity of a Bacillus 1,3-1,4-beta-glucanase. J Mol Biol 2006; 357:1211-25. [PMID: 16483609 DOI: 10.1016/j.jmb.2006.01.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 12/30/2005] [Accepted: 01/04/2006] [Indexed: 10/25/2022]
Abstract
Depolymerization of polysaccharides is catalyzed by highly specific enzymes that promote hydrolysis of the scissile glycosidic bond by an activated water molecule. 1,3-1,4-beta-Glucanases selectively cleave beta-1,4 glycosidic bonds in 3-O-substituted glucopyranosyl units within polysaccharides with mixed linkage. The reaction follows a double-displacement mechanism by which the configuration of the anomeric C(1)-atom of the glucosyl unit in subsite -I is retained. Here we report the high-resolution crystal structure of the hybrid 1,3-1,4-beta-glucanase H(A16-M)(E105Q/E109Q) in complex with a beta-glucan tetrasaccharide. The structure shows four beta-d-glucosyl moieties bound to the substrate-binding cleft covering subsites -IV to -I, thus corresponding to the reaction product. The ten active-site residues Asn26, Glu63, Arg65, Phe92, Tyr94, Glu105, Asp107, Glu109, Asn182 and Trp184 form a network of hydrogen bonds and hydrophobic stacking interactions with the substrate. These residues were previously identified by mutational analysis as significant for stabilization of the enzyme-carbohydrate complex, with Glu105 and Glu109 being the catalytic residues. Compared to the Michaelis complex model, the tetrasaccharide moiety is slightly shifted toward that part of the cleft binding the non-reducing end of the substrate, but shows previously unanticipated strong stacking interactions with Phe92 in subsite -I. A number of specific hydrogen-bond contacts between the enzyme and the equatorial O(2), O(3) and O(6) hydroxyl groups of the glucosyl residues in subsites -I, -II and -III are the structural basis for the observed substrate specificity of 1,3-1,4-beta-glucanases. Kinetic analysis of enzyme variants with the all beta-1,3 linked polysaccharide laminarin identified key residues mediating substrate specificity in good agreement with the structural data. The comparison with structures of the apo-enzyme H(A16-M) and a covalent enzyme-inhibitor (E.I) complex, together with kinetic and mutagenesis data, yields new insights into the structural requirements for substrate binding and catalysis. A detailed view of enzyme-carbohydrate interactions is presented and mechanistic implications are discussed.
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Affiliation(s)
- Olaf J Gaiser
- Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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17
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Biarnés X, Nieto J, Planas A, Rovira C. Substrate Distortion in the Michaelis Complex of Bacillus 1,3–1,4-β-Glucanase. J Biol Chem 2006; 281:1432-41. [PMID: 16260784 DOI: 10.1074/jbc.m507643200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.
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Affiliation(s)
- Xevi Biarnés
- Centre especial de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain
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Abel M, Iversen K, Planas A, Christensen U. Pre-steady-state kinetics of Bacillus licheniformis 1,3-1,4-beta-glucanase: evidence for a regulatory binding site. Biochem J 2003; 371:997-1003. [PMID: 12568655 PMCID: PMC1223346 DOI: 10.1042/bj20021504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2002] [Revised: 01/17/2003] [Accepted: 02/04/2003] [Indexed: 11/17/2022]
Abstract
In a previous paper, we reported the first stopped-flow experiments on a Bacillus licheniformis 1,3-1,4-beta-glucanase [Abel, Planas and Christensen (2001) Biochem. J. 357, 195-202]. It was shown that the pre-steady-state kinetics of the 1,3-1,4-beta-glucanase using the substrate 4-methylumbelliferyl 3-O-beta-cellobiosyl-beta-D-glucoside may be explained by a reaction scheme involving an induced fit and the binding of two substrates as well as a second enzymic conformational change, whereas the results definitely could not be explained in terms of the simple double-displacement scheme. In the present study, we report further stopped-flow kinetic results on the glucanase using a series of low-molecular-mass substrates with various leaving groups and varying chain length. The analysis of the resulting data leads to the conclusion that the free enzyme exists in two conformations, one of which binds the substrates rather strongly in a regulatory site, before any productive interactions can take place. This corresponds to an allosteric activation mechanism. With these substrates, however, the productive enzyme-substrate species are also able to change into less active or inactive forms. This may be seen as a feedback inhibitory mechanism.
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Affiliation(s)
- Mireia Abel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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Faijes M, Fairweather JK, Driguez H, Planas A. Oligosaccharide synthesis by coupled endo-glycosynthases of different specificity: a straightforward preparation of two mixed-linkage hexasaccharide substrates of 1,3/1,4-beta-glucanases. Chemistry 2001; 7:4651-5. [PMID: 11757657 DOI: 10.1002/1521-3765(20011105)7:21<4651::aid-chem4651>3.0.co;2-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Glycosynthases are engineered glycosidases which are hydrolytically inactive yet efficiently catalyse transglycosylation reactions of glycosyl fluoride donors, and are thus promising tools for the enzymatic synthesis of oligosaccharides. Two endo-glycosynthases, the E134A mutant of 1,3/1,4-beta-glucanase from Bacillus licheniformis and the E197A mutant of cellulase Cel7B from Humicola insolens, were used in coupled reactions for the stepwise synthesis of hexasaccharide substrates of 1,3/1,4-beta-glucanases. Because the two endo-glycosynthases show different specificity, towards laminaribiosyl and cellobiosyl donors, respectively, the target hexasaccharides were prepared by condensation of the corresponding disaccharide building blocks through sequential addition of the glycosynthases in a "one-pot" process. Different strategies were used to achieve the desired transglycosylation between donor and acceptor in each step, and to prevent unwanted elongation of the first condensation product and polymerization (self-condensation) of the donor: 1) selection of disaccharide donors differing in the configuration of the hydroxyl substituent normally acting as acceptor, 2) temporary protection of the polymerizable hydroxyl group of the donor, or 3) addition of an excess of acceptor to decrease the probability that the donor can act as an acceptor. The best procedure involved the condensation of alpha-lactosyl or 4II-O-tetrahydropyranyl-alpha-cellobiosyl fluorides with alpha-laminaribiosyl fluoride, catalyzed by E197A Cel7B, to give tetrasaccharide fluorides, which were then the donors for in situ condensation with methyl beta-cellobioside catalyzed by E134A 1,3/1,4-beta-glucanase. After isolation, the final hexasaccharides Gal/beta4Glcbeta4Glcbeta3Glcbeta4Glcbeta4Glcbeta-OMe and Glcbeta4Glcbeta4Glcbeta3Glcbeta4Glcbeta4-Glcbeta-OMe were obtained in 70-80% overall yields.
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Affiliation(s)
- M Faijes
- Laboratori de Bioquímica, Institut Químic de Sarrià Universitat Ramon Llull, Barcelona, Spain
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Planas A. Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1543:361-382. [PMID: 11150614 DOI: 10.1016/s0167-4838(00)00231-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
1,3-1,4-beta-Glucanases (or lichenases, EC 3.2.1.73) hydrolyse linear beta-glucans containing beta-1,3 and beta-1,4 linkages such as cereal beta-glucans and lichenan, with a strict cleavage specificity for beta-1,4 glycosidic bonds on 3-O-substituted glucosyl residues. The bacterial enzymes are retaining glycosyl hydrolases of family 16 with a jellyroll beta-sandwich fold and a substrate binding cleft composed of six subsites. The present paper reviews the structure-function aspects of the enzymatic action including mechanistic enzymology, protein engineering and X-ray crystallographic studies.
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Affiliation(s)
- A Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 390, 08017, Barcelona, Spain.
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