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Febbraio F, Ionata E, Marcolongo L. Forty years of study on the thermostable β-glycosidase from S. solfataricus: Production, biochemical characterization and biotechnological applications. Biotechnol Appl Biochem 2020; 67:602-618. [PMID: 32621790 DOI: 10.1002/bab.1982] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of this paper is to make the point on the fortieth years study on the β-glycosidase from Sulfolobus solfataricus. This enzyme represents one of the thermophilic biocatalysts, which is more extensively studied as witnessed by the numerous literature reports available since 1980. Comprehensive biochemical studies highlighted its broad substrate specificity for β-d-galacto-, gluco-, and fuco-sides and also showed its remarkable exo-glucosidase and transglycosidase activities. The enzyme demonstrated to be active and stable over a wide range of temperature and pHs, withstanding to several drastic conditions comprising solvents and detergents. Over the years, a great deal of studies were focused on its homotetrameric tridimensional structure, elucidating several structural features involved in the enzyme stability, such as ion pairs and post-translational modifications. Several β-glycosidase mutants were produced in the years in order to understand its peculiar behavior in extreme conditions and/or to improve its functional properties. The β-glycosidase overproduction was also afforded reporting numerous studies dealing with its production in the mesophilic host Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, and Lactococcus lactis. Relevant applications in food, beverages, bioenergy, pharmaceuticals, and nutraceutical fields of this enzyme, both in free and immobilized forms, highlighted its biotechnological relevance.
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Affiliation(s)
- Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Naples, Italy
| | - Elena Ionata
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
| | - Loredana Marcolongo
- Research Institute on Terrestrial Ecosystems, National Research Council (CNR), Naples, 80131, Italy
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Wang D, Kim H, Lee S, Kim DH, Joe MH. High-level production of poly-γ-glutamic acid from untreated molasses by Bacillus siamensis IR10. Microb Cell Fact 2020; 19:101. [PMID: 32398084 PMCID: PMC7216703 DOI: 10.1186/s12934-020-01361-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Background Poly-γ-glutamic acid (γ-PGA) is a promising biopolymer and has been applied in many fields. Bacillus siamensis SB1001 was a newly isolated poly-γ-glutamic acid producer with sucrose as its optimal carbon source. To improve the utilization of carbon source, and then molasses can be effectively used for γ-PGA production, 60cobalt gamma rays was used to mutate the genes of B. siamensis SB1001. Results Bacillus siamensis IR10 was screened for the production of γ-PGA from untreated molasses. In batch fermentation, 17.86 ± 0.97 g/L γ-PGA was obtained after 15 h, which is 52.51% higher than that of its parent strain. Fed-batch fermentation was performed to further improve the yield of γ-PGA with untreated molasses, yielding 41.40 ± 2.01 g/L of γ-PGA with a productivity of 1.73 ± 0.08 g/L/h. An average γ-PGA productivity of 1.85 g/L/h was achieved in the repeated fed-batch fermentation. This is the first report of such a high γ-PGA productivity. The analysis of the enzyme activities showed that they were affected by the carbon sources, enhanced ICDH and GDH, and decreased ODHC, which are important for γ-PGA production. Conclusion These results suggest that untreated molasses can be used for economical and industrial-scale production of γ-PGA by B. siamensis IR10.![]()
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Affiliation(s)
- Dexin Wang
- Radiation Utilization and Facilities Management Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea.,Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics,Center for Fungal Pathogenesis, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Hyangmi Kim
- Bacteria Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, 37242, Republic of Korea
| | - Sungbeom Lee
- Radiation Research Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Dae-Hyuk Kim
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics,Center for Fungal Pathogenesis, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Min-Ho Joe
- Radiation Utilization and Facilities Management Division, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Republic of Korea.
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Lansky S, Zehavi A, Belrhali H, Shoham Y, Shoham G. Structural basis for enzyme bifunctionality – the case of Gan1D fromGeobacillus stearothermophilus. FEBS J 2017; 284:3931-3953. [DOI: 10.1111/febs.14283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Shifra Lansky
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | | | - Yuval Shoham
- Department of Biotechnology and Food Engineering Technion ‐ Israel Institute of Technology Haifa Israel
| | - Gil Shoham
- Institute of Chemistry The Laboratory for Structural Chemistry and Biology The Hebrew University of Jerusalem Israel
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4
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Acebrón I, Plaza-Vinuesa L, de Las Rivas B, Muñoz R, Cumella J, Sánchez-Sancho F, Mancheño JM. Structural basis of the substrate specificity and instability in solution of a glycosidase from Lactobacillus plantarum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1227-1236. [PMID: 28734976 DOI: 10.1016/j.bbapap.2017.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 01/06/2023]
Abstract
Statistics from structural genomics initiatives reveal that around 50-55% of the expressed, non-membrane proteins cannot be purified and therefore structurally characterized due to solubility problems, which emphasized protein solubility as one of the most serious concerns in structural biology projects. Lactobacillus plantarum CECT 748T produces an aggregation-prone glycosidase (LpBgl) that we crystallized previously. However, this result could not be reproduced due to protein instability and therefore further high-resolution structural analyses of LpBgl were impeded. The obtained crystals of LpBgl diffracted up to 2.48Å resolution and permitted to solve the structure of the enzyme. Analysis of the active site revealed a pocket for phosphate-binding with an uncommon architecture, where a phosphate molecule is tightly bound suggesting the recognition of 6-phosphoryl sugars. In agreement with this observation, we showed that LpBgl exhibited 6-phospho-β-glucosidase activity. Combination of structural and mass spectrometry results revealed the formation of dimethyl arsenic adducts on the solvent exposed cysteine residues Cys211 and Cys292. Remarkably, the double mutant Cys211Ser/Cys292Ser resulted stable in solution at high concentrations indicating that the marginal solubility of LpBgl can be ascribed specifically to these two cysteine residues. The 2.30Å crystal structure of this double mutant showed no disorder around the newly incorporated serine residues and also loop rearrangements within the phosphate-binding site. Notably, LpBgl could be prepared at high yield by proteolytic digestion of the fusion protein LSLt-LpBgl, which raises important questions about potential hysteretic processes upon its initial production as an enzyme fused to a solubility enhancer.
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Affiliation(s)
- Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Blanca de Las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - J Cumella
- Institute of Medicinal Chemistry (CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - F Sánchez-Sancho
- Institute of Medicinal Chemistry (CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain.
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Koudounas K, Banilas G, Michaelidis C, Demoliou C, Rigas S, Hatzopoulos P. A defence-related Olea europaea β-glucosidase hydrolyses and activates oleuropein into a potent protein cross-linking agent. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2093-106. [PMID: 25697790 PMCID: PMC4669557 DOI: 10.1093/jxb/erv002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Oleuropein, the major secoiridoid compound in olive, is involved in a sophisticated two-component defence system comprising a β-glucosidase enzyme that activates oleuropein into a toxic glutaraldehyde-like structure. Although oleuropein deglycosylation studies have been monitored extensively, an oleuropein β-glucosidase gene has not been characterized as yet. Here, we report the isolation of OeGLU cDNA from olive encoding a β-glucosidase belonging to the defence-related group of terpenoid-specific glucosidases. In planta recombinant protein expression assays showed that OeGLU deglycosylated and activated oleuropein into a strong protein cross-linker. Homology and docking modelling predicted that OeGLU has a characteristic (β/α)8 TIM barrel conformation and a typical construction of a pocket-shaped substrate recognition domain composed of conserved amino acids supporting the β-glucosidase activity and non-conserved residues associated with aglycon specificity. Transcriptional analysis in various olive organs revealed that the gene was developmentally regulated, with its transcript levels coinciding well with the spatiotemporal patterns of oleuropein degradation and aglycon accumulation in drupes. OeGLU upregulation in young organs reflects its prominent role in oleuropein-mediated defence system. High gene expression during drupe maturation implies an additional role in olive secondary metabolism, through the degradation of oleuropein and reutilization of hydrolysis products.
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Affiliation(s)
| | - Georgios Banilas
- Department of Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, 12210 Athens, Greece
| | - Christos Michaelidis
- Department of Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece University of Nicosia Research Foundation, University of Nicosia, 1700 Nicosia, Cyprus
| | - Catherine Demoliou
- University of Nicosia Research Foundation, University of Nicosia, 1700 Nicosia, Cyprus
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, 118 55 Athens, Greece
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6
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Lansky S, Zehavi A, Dann R, Dvir H, Belrhali H, Shoham Y, Shoham G. Purification, crystallization and preliminary crystallographic analysis of Gan1D, a GH1 6-phospho-β-galactosidase from Geobacillus stearothermophilus T1. Acta Crystallogr F Struct Biol Commun 2014; 70:225-31. [PMID: 24637762 PMCID: PMC3936444 DOI: 10.1107/s2053230x13034778] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 12/28/2013] [Indexed: 11/10/2022] Open
Abstract
Geobacillus stearothermophilus T1 is a Gram-positive thermophilic soil bacterium that contains an extensive system for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. The bacterium uses a number of extracellular enzymes that break down the high-molecular-weight polysaccharides into short oligosaccharides, which enter the cell and are further hydrolyzed into sugar monomers by dedicated intracellular glycoside hydrolases. The interest in the biochemical characterization and structural analysis of these proteins originates mainly from the wide range of their potential biotechnological applications. Studying the different hemicellulolytic utilization systems in G. stearothermophilus T1, a new galactan-utilization gene cluster was recently identified, which encodes a number of proteins, one of which is a GH1 putative 6-phospho-β-galactosidase (Gan1D). Gan1D has recently been cloned, overexpressed, purified and crystallized as part of its comprehensive structure-function study. The best crystals obtained for this enzyme belonged to the triclinic space group P1, with average crystallographic unit-cell parameters of a = 67.0, b = 78.1, c = 92.1 Å, α = 102.4, β = 93.5, γ = 91.7°. A full diffraction data set to 1.33 Å resolution has been collected for the wild-type enzyme, as measured from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for the detailed three-dimensional crystal structure analysis of Gan1D.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Arie Zehavi
- Department of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Roie Dann
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hay Dvir
- Technion Center for Structural Biology, The Lorry I. Lokey Interdisciplinary Center for Life Science and Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Hassan Belrhali
- European Molecular Biology Laboratory, Grenoble Outstation, and Unit for Virus–Host Cell Interactions, European Synchrotron Radiation Facility, Université Grenoble Alpes–EMBL–CNRS, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | - Gil Shoham
- Institute of Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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7
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Banner DW, Gsell B, Benz J, Bertschinger J, Burger D, Brack S, Cuppuleri S, Debulpaep M, Gast A, Grabulovski D, Hennig M, Hilpert H, Huber W, Kuglstatter A, Kusznir E, Laeremans T, Matile H, Miscenic C, Rufer AC, Schlatter D, Steyaert J, Stihle M, Thoma R, Weber M, Ruf A. Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1124-37. [DOI: 10.1107/s0907444913006574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/07/2013] [Indexed: 01/11/2023]
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8
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Yu WL, Jiang YL, Pikis A, Cheng W, Bai XH, Ren YM, Thompson J, Zhou CZ, Chen Y. Structural insights into the substrate specificity of a 6-phospho-β-glucosidase BglA-2 from Streptococcus pneumoniae TIGR4. J Biol Chem 2013; 288:14949-58. [PMID: 23580646 DOI: 10.1074/jbc.m113.454751] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 6-phospho-β-glucosidase BglA-2 (EC 3.2.1.86) from glycoside hydrolase family 1 (GH-1) catalyzes the hydrolysis of β-1,4-linked cellobiose 6-phosphate (cellobiose-6'P) to yield glucose and glucose 6-phosphate. Both reaction products are further metabolized by the energy-generating glycolytic pathway. Here, we present the first crystal structures of the apo and complex forms of BglA-2 with thiocellobiose-6'P (a non-metabolizable analog of cellobiose-6'P) at 2.0 and 2.4 Å resolution, respectively. Similar to other GH-1 enzymes, the overall structure of BglA-2 from Streptococcus pneumoniae adopts a typical (β/α)8 TIM-barrel, with the active site located at the center of the convex surface of the β-barrel. Structural analyses, in combination with enzymatic data obtained from site-directed mutant proteins, suggest that three aromatic residues, Tyr(126), Tyr(303), and Trp(338), at subsite +1 of BglA-2 determine substrate specificity with respect to 1,4-linked 6-phospho-β-glucosides. Moreover, three additional residues, Ser(424), Lys(430), and Tyr(432) of BglA-2, were found to play important roles in the hydrolytic selectivity toward phosphorylated rather than non-phosphorylated compounds. Comparative structural analysis suggests that a tryptophan versus a methionine/alanine residue at subsite -1 may contribute to the catalytic and substrate selectivity with respect to structurally similar 6-phospho-β-galactosidases and 6-phospho-β-glucosidases assigned to the GH-1 family.
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Affiliation(s)
- Wei-Li Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui 230027, China
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9
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Michalska K, Tan K, Li H, Hatzos-Skintges C, Bearden J, Babnigg G, Joachimiak A. GH1-family 6-P-β-glucosidases from human microbiome lactic acid bacteria. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:451-63. [PMID: 23519420 PMCID: PMC3605045 DOI: 10.1107/s0907444912049608] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/03/2012] [Indexed: 11/11/2022]
Abstract
In lactic acid bacteria and other bacteria, carbohydrate uptake is mostly governed by phosphoenolpyruvate-dependent phosphotransferase systems (PTSs). PTS-dependent translocation through the cell membrane is coupled with phosphorylation of the incoming sugar. After translocation through the bacterial membrane, the β-glycosidic bond in 6'-P-β-glucoside is cleaved, releasing 6-P-β-glucose and the respective aglycon. This reaction is catalyzed by 6-P-β-glucosidases, which belong to two glycoside hydrolase (GH) families: GH1 and GH4. Here, the high-resolution crystal structures of GH1 6-P-β-glucosidases from Lactobacillus plantarum (LpPbg1) and Streptococcus mutans (SmBgl) and their complexes with ligands are reported. Both enzymes show hydrolytic activity towards 6'-P-β-glucosides. The LpPbg1 structure has been determined in an apo form as well as in a complex with phosphate and a glucose molecule corresponding to the aglycon molecule. The S. mutans homolog contains a sulfate ion in the phosphate-dedicated subcavity. SmBgl was also crystallized in the presence of the reaction product 6-P-β-glucose. For a mutated variant of the S. mutans enzyme (E375Q), the structure of a 6'-P-salicin complex has also been determined. The presence of natural ligands enabled the definition of the structural elements that are responsible for substrate recognition during catalysis.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
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Characterization of a novel metagenome-derived 6-phospho-β-glucosidase from black liquor sediment. Appl Environ Microbiol 2013; 79:2121-7. [PMID: 23335769 DOI: 10.1128/aem.03528-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enzyme 6-phospho-β-glucosidase is an important member of the glycoside hydrolase family 1 (GH1). However, its catalytic mechanisms, especially the key residues determining substrate specificity and affinity, are poorly understood. A metagenome-derived gene sequence, encoding a novel 6-phospho-β-glucosidase designated Pbgl25-217, was isolated and characterized. The optimal conditions for enzymatic activity were 37°C and pH 7; Ca(2+), Mg(2+), and Mn(2+) stabilized the activity of Pbgl25-217, whereas Ni(2+), Fe(2+), Zn(2+), Cu(2+), and Fe(3+) inhibited its activity. The Km and Vmax of Pbgl25-217 were 4.8 mM and 1,987.0 U mg(-1), respectively. Seven conserved residues were recognized by multiple alignments and were tested by site-directed mutagenesis for their functions in substrate recognition and catalytic reaction. The results suggest that residues S427, Lys435, and Tyr437 act as "gatekeepers" in a phosphate-binding loop and play important roles in phosphate recognition. This functional identification may provide insights into the specificity of 6-phospho-β-glycosidases in GH1 and be useful for designing further directed evolution.
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11
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Stepper J, Dabin J, Eklof JM, Thongpoo P, Kongsaeree P, Taylor EJ, Turkenburg JP, Brumer H, Davies GJ. Structure and activity of the Streptococcus pyogenes family GH1 6-phospho-β-glucosidase SPy1599. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:16-23. [PMID: 23275159 DOI: 10.1107/s0907444912041005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/28/2012] [Indexed: 01/14/2023]
Abstract
The group A streptococcus Streptococcus pyogenes is the causative agent of a wide spectrum of invasive infections, including necrotizing fasciitis, scarlet fever and toxic shock syndrome. In the context of its carbohydrate chemistry, it is interesting that S. pyogenes (in this work strain M1 GAS SF370) displays a spectrum of oligosaccharide-processing enzymes that are located in close proximity on the genome but that the in vivo function of these proteins remains unknown. These proteins include different sugar transporters (SPy1593 and SPy1595), both GH125 α-1,6- and GH38 α-1,3-mannosidases (SPy1603 and SPy1604), a GH84 β-hexosaminidase (SPy1600) and a putative GH2 β-galactosidase (SPy1586), as well as SPy1599, a family GH1 `putative β-glucosidase'. Here, the solution of the three-dimensional structure of SPy1599 in a number of crystal forms complicated by unusual crystallographic twinning is reported. The structure is a classical (β/α)(8)-barrel, consistent with CAZy family GH1 and other members of the GH-A clan. SPy1599 has been annotated in sequence depositions as a β-glucosidase (EC 3.2.1.21), but no such activity could be found; instead, three-dimensional structural overlaps with other enzymes of known function suggested that SPy1599 contains a phosphate-binding pocket in the active site and has possible 6-phospho-β-glycosidase activity. Subsequent kinetic analysis indeed showed that SPy1599 has 6-phospho-β-glucosidase (EC 3.2.1.86) activity. These data suggest that SPy1599 is involved in the intracellular degradation of 6-phosphoglycosides, which are likely to originate from import through one of the organism's many phosphoenolpyruvate phosphotransfer systems (PEP-PTSs).
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Affiliation(s)
- Judith Stepper
- Department of Chemistry, University of York, Heslington, York YO10 5DD, England
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12
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Zheng B, Yang W, Zhao X, Wang Y, Lou Z, Rao Z, Feng Y. Crystal structure of hyperthermophilic endo-β-1,4-glucanase: implications for catalytic mechanism and thermostability. J Biol Chem 2011; 287:8336-46. [PMID: 22128157 DOI: 10.1074/jbc.m111.266346] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endo-β-1,4-glucanase from thermophilic Fervidobacterium nodosum Rt17-B1 (FnCel5A), a new member of glycosyl hydrolase family 5, is highly thermostable and exhibits the highest activity on carboxymethylcellulose among the reported homologues. To understand the structural basis for the thermostability and catalytic mechanism, we report here the crystal structures of FnCel5A and the complex with glucose at atomic resolution. FnCel5A exhibited a (β/α)(8)-barrel structure typical of clan GH-A of the glycoside hydrolase families with a large and deep catalytic pocket located in the C-terminal end of the β-strands that may permit substrate access. A comparison of the structure of FnCel5A with related structures from thermopile Clostridium thermocellum, mesophile Clostridium cellulolyticum, and psychrophile Pseudoalteromonas haloplanktis showed significant differences in intramolecular interactions (salt bridges and hydrogen bonds) that may account for the difference in their thermostabilities. The substrate complex structure in combination with a mutagenesis analysis of the catalytic residues implicates a distinctive catalytic module Glu(167)-His(226)-Glu(283), which suggests that the histidine may function as an intermediate for the electron transfer network between the typical Glu-Glu catalytic module. Further investigation suggested that the aromatic residues Trp(61), Trp(204), Phe(231), and Trp(240) as well as polar residues Asn(51), His(127), Tyr(228), and His(235) in the active site not only participated in substrate binding but also provided a unique microenvironment suitable for catalysis. These results provide substantial insight into the unique characteristics of FnCel5A for catalysis and adaptation to extreme temperature.
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Affiliation(s)
- Baisong Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China
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13
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Structural stability and unfolding transition of β-glucosidases: a comparative investigation on isozymes from a thermo-tolerant yeast. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:877-89. [DOI: 10.1007/s00249-011-0706-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/04/2011] [Accepted: 04/08/2011] [Indexed: 11/26/2022]
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14
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Kumar R, Kumar S, Sangwan S, Yadav IS, Yadav R. Protein modeling and active site binding mode interactions of myrosinase–sinigrin in Brassica juncea—An in silico approach. J Mol Graph Model 2011; 29:740-6. [DOI: 10.1016/j.jmgm.2010.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 11/28/2010] [Accepted: 12/07/2010] [Indexed: 11/15/2022]
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15
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Seshadri S, Akiyama T, Opassiri R, Kuaprasert B, Cairns JK. Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides. PLANT PHYSIOLOGY 2009; 151:47-58. [PMID: 19587102 PMCID: PMC2735989 DOI: 10.1104/pp.109.139436] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 07/02/2009] [Indexed: 05/18/2023]
Abstract
Glycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides.
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Affiliation(s)
- Supriya Seshadri
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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16
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Turan Y. A pseudo-beta-glucosidase in Arabidopsis thaliana: correction by site-directed mutagenesis, heterologous expression, purification, and characterization. BIOCHEMISTRY (MOSCOW) 2008; 73:912-9. [PMID: 18774938 DOI: 10.1134/s0006297908080099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Since At2g25630 is an intronless gene with a premature stop codon, its cDNA encoding the predicted mature beta-glucosidase isoenzyme was synthesized from the previously isolated Arabidopsis thaliana genomic DNA. The stop codon was converted to a sense codon by site-directed mutagenesis. The native and mutated cDNA sequences were separately cloned into the vector pPICZalphaB and expressed in Pichia pastoris. Only the cells transformed with mutated cDNA-vector construct produced the active protein. The mutated recombinant beta-glucosidase isoenzyme was chromatographically purified to apparent homogeneity. The molecular mass of the protein is estimated as ca. 60 kD by SDS-PAGE. The pH optimum of activity is 5.6, and it is fairly stable in the pH range of 5.0-8.5. The purified recombinant beta-glucosidase is effectively active on para-/ortho-nitrophenyl-beta-D-glucopyranosides (p-/o-NPG) and 4-methylumbelliferyl-beta-D-glucopyranoside (4-MUG) with K(m) values of 1.9, 2.1, 0.78 mM and k(cat) values of 114, 106, 327 nkat/mg, respectively. It also exhibits different levels of activity against para-/ortho-nitrophenyl-beta-D-fucopyranosides (p-/o-NPF), amygdalin, prunasin, cellobiose, gentiobiose, and salicin. The enzyme is competitively inhibited by gluconolactone and p-nitrophenyl-1-thio-beta-D-glucopyranoside with p-NPG, o-NPG, and 4-MUG as substrates. The enzyme is found to be very tolerant to glucose inhibition. The catalytic role of nucleophilic glutamic acid in the motif YITENG of beta-glucosidases and mutated recombinant enzyme is discussed.
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Affiliation(s)
- Y Turan
- Balikesir University, Arts and Sciences Faculty, Department of Biology, Cagis Kampusu, Balikesir, Turkey.
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17
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León M, Isorna P, Menéndez M, Sanz-Aparicio J, Polaina J. Comparative study and mutational analysis of distinctive structural elements of hyperthermophilic enzymes. Protein J 2007; 26:435-44. [PMID: 17503162 DOI: 10.1007/s10930-007-9083-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Comparison of the three-dimensional structure of hyperthermophilic and mesophilic beta-glycosidases shows differences in secondary structure composition. The enzymes from hyperthermophilic archaea have a significantly larger number of beta-strands arranged in supernumerary beta-sheets compared to mesophilic enzymes from bacteria and other organisms. Amino acid replacements designed to alter the structure of the supernumerary beta-strands were introduced by site directed mutagenesis into the sequence encoding the beta-glycosidase from Sulfolobus solfataricus. Most of the replacements caused almost complete loss of activity but some yielded enzyme variants whose activities were affected specifically at higher temperatures. Far-UV CD spectra recorded as a function of temperature for both wild type beta-glycosidase and mutant V349G, one of the mutants with reduced activity at higher temperatures, were similar, showing that the protein structure of the mutant was stable at the highest temperatures assayed. The properties of mutant V349G show a difference between thermostability (stability of the protein structure at high temperatures) and thermophilicity (optimal activity at high temperatures).
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Affiliation(s)
- Maela León
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apdo. de Correos 73, Burjassot, Valencia, E46100, Spain
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18
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Tribolo S, Berrin JG, Kroon PA, Czjzek M, Juge N. The Crystal Structure of Human Cytosolic β-Glucosidase Unravels the Substrate Aglycone Specificity of a Family 1 Glycoside Hydrolase. J Mol Biol 2007; 370:964-75. [PMID: 17555766 DOI: 10.1016/j.jmb.2007.05.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 04/27/2007] [Accepted: 05/12/2007] [Indexed: 11/22/2022]
Abstract
Human cytosolic beta-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. In this study, the substrate preference of this enzyme was investigated by mutational analysis, X-ray crystallography and homology modelling. The crystal structure of hCBG was solved by the molecular replacement method and refined at 2.7 A resolution. The main-chain fold of the enzyme belongs to the (beta/alpha)(8) barrel structure, which is common to family 1 glycoside hydrolases. The active site is located at the bottom of a pocket (about 16 A deep) formed by large surface loops, surrounding the C termini of the barrel of beta-strands. As for all the clan of GH-A enzymes, the two catalytic glutamate residues are located on strand 4 (the acid/base Glu165) and on strand 7 (the nucleophile Glu373). Although many features of hCBG were shown to be very similar to previously described enzymes from this family, crucial differences were observed in the surface loops surrounding the aglycone binding site, and these are likely to strongly influence the substrate specificity. The positioning of a substrate molecule (quercetin-4'-glucoside) by homology modelling revealed that hydrophobic interactions dominate the binding of the aglycone moiety. In particular, Val168, Trp345, Phe225, Phe179, Phe334 and Phe433 were identified as likely to be important in determining substrate specificity in hCBG, and site-directed mutagenesis supported a key role for some of these residues.
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Affiliation(s)
- Sandra Tribolo
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
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19
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Isorna P, Polaina J, Latorre-García L, Cañada FJ, González B, Sanz-Aparicio J. Crystal structures of Paenibacillus polymyxa beta-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. J Mol Biol 2007; 371:1204-18. [PMID: 17585934 DOI: 10.1016/j.jmb.2007.05.082] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/22/2007] [Accepted: 05/25/2007] [Indexed: 11/19/2022]
Abstract
Bacteria species involved in degradation of cellulosic substrates produce a variety of enzymes for processing related compounds along the hydrolytic pathway. Paenibacillus polymyxa encodes two homologous beta-glucosidases, BglA and BglB, presenting different quaternary structures and substrate specificities. We previously reported the 3D-structure of BglA, which is highly specific against cellobiose. Here, we present structural analysis of BglB, a monomeric enzyme that acts as an exo-beta-glucosidase hydrolyzing cellobiose and cellodextrins of higher degree of polymerization. The crystal structure of BglB shows that several polar residues narrow the active site pocket and contour additional subsites. The structure of the BglB-cellotetraose complex confirms these subsites, revealing the substrate-binding mode, and shows the oligosaccharide-enzyme recognition pattern in detail. Comparison between BglA and BglB crystal structures suggests that oligomerization in BglA can assist in fine-tuning the specificity of the active centre by modulating the loops surrounding the cavity. We have solved the crystal structure of BglB with bound thiocellobiose, a competitive inhibitor, which together with the BglB-cellotetraose complex delineate the general features of the aglycon site. The detailed characterization of the atomic interactions at the aglycon site show a recognition pattern common to all bacterial beta-glucosidases, and presents some differences with the aglycon site in plant beta-glycosidases essentially by means of a different orientation of the basal Trp. The crystal structures of of BglB with a covalently bound inhibitor (derived from 2-fluoroglucoside) and glucose (produced by hydrolysis of the substrate in the crystal), provide additional pictures of the binding events and the intermediates formed during the reaction. Altogether, this information can assist in the understanding of subtle differences of the enzyme mechanism and substrate recognition within this family of enzymes, and consequently it can help in the development of new enzymes with improved activity or specificity.
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Affiliation(s)
- Pablo Isorna
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006-Madrid, Spain
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20
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Vilei EM, Correia I, Ferronha MH, Bischof DF, Frey J. Beta-D-glucoside utilization by Mycoplasma mycoides subsp. mycoides SC: possible involvement in the control of cytotoxicity towards bovine lung cells. BMC Microbiol 2007; 7:31. [PMID: 17439646 PMCID: PMC1855930 DOI: 10.1186/1471-2180-7-31] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 04/17/2007] [Indexed: 12/20/2022] Open
Abstract
Background Contagious bovine pleuropneumonia (CBPP) caused by Mycoplasma mycoides subsp. mycoides small-colony type (SC) is among the most serious threats for livestock producers in Africa. Glycerol metabolism-associated H2O2 production seems to play a crucial role in virulence of this mycoplasma. A wide number of attenuated strains of M. mycoides subsp. mycoides SC are currently used in Africa as live vaccines. Glycerol metabolism is not affected in these vaccine strains and therefore it does not seem to be the determinant of their attenuation. A non-synonymous single nucleotide polymorphism (SNP) in the bgl gene coding for the 6-phospho-β-glucosidase (Bgl) has been described recently. The SNP differentiates virulent African strains isolated from outbreaks with severe CBPP, which express the Bgl isoform Val204, from strains to be considered less virulent isolated from CBPP outbreaks with low mortality and vaccine strains, which express the Bgl isoform Ala204. Results Strains of M. mycoides subsp. mycoides SC considered virulent and possessing the Bgl isoform Val204, but not strains with the Bgl isoform Ala204, do trigger elevated levels of damage to embryonic bovine lung (EBL) cells upon incubation with the disaccharides (i.e., β-D-glucosides) sucrose and lactose. However, strains expressing the Bgl isoform Val204 show a lower hydrolysing activity on the chromogenic substrate p-nitrophenyl-β-D-glucopyranoside (pNPbG) when compared to strains that possess the Bgl isoform Ala204. Defective activity of Bgl in M. mycoides subsp. mycoides SC does not lead to H2O2 production. Rather, the viability during addition of β-D-glucosides in medium-free buffers is higher for strains harbouring the Bgl isoform Val204 than for those with the isoform Ala204. Conclusion Our results indicate that the studied SNP in the bgl gene is one possible cause of the difference in bacterial virulence among strains of M. mycoides subsp. mycoides SC. Bgl does not act as a direct virulence factor, but strains possessing the Bgl isoform Val204 with low hydrolysing activity are more prone to survive in environments that contain high levels of β-D-glucosides, thus contributing in some extent to mycoplasmaemia.
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Affiliation(s)
- Edy M Vilei
- Institute of Veterinary Bacteriology, University of Bern, Länggass-Strasse 122, Postfach, CH-3001 Bern, Switzerland
| | - Ivone Correia
- Laboratório Nacional de Investigação Veterinária, Departamento de Biologia Celular, Estrada de Benfica 701, P-1549-011 Lisbon, Portugal
| | - M Helena Ferronha
- Laboratório Nacional de Investigação Veterinária, Departamento de Biologia Celular, Estrada de Benfica 701, P-1549-011 Lisbon, Portugal
| | - Daniela F Bischof
- Institute of Veterinary Bacteriology, University of Bern, Länggass-Strasse 122, Postfach, CH-3001 Bern, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Länggass-Strasse 122, Postfach, CH-3001 Bern, Switzerland
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21
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Fleury D, Domaingue P, Gillard C, Touitou R, Mollat P. Expression, purification, characterization and crystallization of a recombinant human cytosolic β-glucosidase produced in insect cells. Protein Expr Purif 2007; 52:96-103. [PMID: 17064932 DOI: 10.1016/j.pep.2006.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 08/18/2006] [Accepted: 08/22/2006] [Indexed: 11/26/2022]
Abstract
Human cytosolic beta-glucosidase is a monomeric enzyme that hydrolyzes various beta-d-glycosides and its real physiological role remains unclear. Here, we describe the production of this enzyme in Sf9 cells with a N-terminal 6x His tag. The production yield of the recombinant protein was in the 10 to 30 mg/l range. The protein was purified to homogeneity using two chromatographic steps, taking advantage of the 6x His tag in the first step, then using the physical and chemical properties of the protein for ionic exchange. Gel filtration analysis revealed that the protein is monomeric as expected. The kinetic parameters for 4-methylumbelliferyl beta-L-glucopyranoside, VM and KM, were measured (KM=32 microM and VM=157 micromol/h/mg at pH 7.0) and found similar to those reported for either the natural isolated enzyme or the recombinant protein expressed in COS7 cells (KM of 60-70 microM and 40 microM, respectively). Protein crystals were obtained and are now under structural investigations. In summary, we set up a heterologous expression system in Sf9 insect cells allowing the expression and production of large amounts of a pure active human protein, suitable for crystallographic studies.
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Affiliation(s)
- Damien Fleury
- Prostrakan, Protein Production and Crystallization, 102 route de Noisy, 93230 Romainville, France.
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22
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Adam AC, Rubio-Texeira M, Polaina J. Lactose: The Milk Sugar from a Biotechnological Perspective. Crit Rev Food Sci Nutr 2005; 44:553-7. [PMID: 15969327 DOI: 10.1080/10408690490931411] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Lactose is a very important sugar because of its abundance in the milk of humans and domestic animals. Lactose is a valuable asset as a basic nutrient and the main substrate in fermentative processes that led to the production of fermented milk products, such as yogurt and kefir. In some instances, lactose also can be a problem as the causative agent of some diseases, such as lactose intolerance and galactosemia, or for being a by-product generated in huge amounts by the cheese industry. The study of the biochemical reactions leading to the synthesis and assimilation of lactose has provided valuable models for the understanding of biosynthetic and catabolic processes. Lactose-hydrolyzing enzymes are structurally and phylogenetically related to different types of beta-galactosidases and bacterial cellobiases involved in the enzymatic degradation of cellulose. Biotransformation of lactose, by either enzymatic or fermentative procedures, is important for different types of industrial applications in dairy and pharmaceutical industries.
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Affiliation(s)
- Ana C Adam
- Instituto de Agroquímica y Tecnología de Alimentos, Valencia, Spain
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23
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Akiba T, Nishio M, Matsui I, Harata K. X-ray structure of a membrane-bound β-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii. Proteins 2004; 57:422-31. [PMID: 15340929 DOI: 10.1002/prot.20203] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The beta-glycosidase of the hyperthermophilic Archaeon Pyrococcus horikoshii is a membrane-bound enzyme with the preferred substrate of alkyl-beta-glycosides. In this study, the unusual structural features that confer the extreme thermostability and substrate preferences of this enzyme were investigated by X-ray crystallography and docking simulation. The enzyme was crystallized in the presence of a neutral surfactant, and the crystal structure was solved by the molecular replacement method and refined at 2.5 A. The main-chain fold of the enzyme belongs to the (betaalpha)8 barrel structure common to the Family 1 glycosyl hydrolases. The active site is located at the center of the C-termini of the barrel beta-strands. The deep pocket of the active site accepts one sugar unit, and a hydrophobic channel extending radially from there binds the nonsugar moiety of the substrate. The docking simulation for oligosaccharides and alkylglucosides indicated that alkylglucosides with a long aliphatic chain are easily accommodated in the hydrophobic channel. This sparingly soluble enzyme has a cluster of hydrophobic residues on its surface, situated at the distal end of the active site channel and surrounded by a large patch of positively charged residues. We propose that this hydrophobic region can be inserted into the membrane while the surrounding positively charged residues make favorable contacts with phosphate groups on the inner surface of the membrane. The enzyme could thus adhere to the membrane in the proximity of its glycolipid substrate.
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Affiliation(s)
- Toshihiko Akiba
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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24
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Abstract
A C4-symmetric tetrameric aldolase was used to produce a quadratic network consisting of the enzyme as a rigid four-way connector and stiff streptavidin rods as spacers. Each aldolase subunit was furnished with a His6 tag for oriented binding to a planar surface and two tethered biotins for binding streptavidin in an oriented manner. The networks were improved by starting with composite units and also by binding to nickel-nitrilotriacetic acid-lipid monolayers. The mesh was adjustable in 5-nanometer increments. The production of a net with switchable mesh was initiated with the use of a calcium ion-containing beta-helix spacer that denatured on calcium ion depletion.
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Affiliation(s)
- Philippe Ringler
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
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25
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Berrin JG, Czjzek M, Kroon PA, McLauchlan WR, Puigserver A, Williamson G, Juge N. Substrate (aglycone) specificity of human cytosolic beta-glucosidase. Biochem J 2003; 373:41-8. [PMID: 12667141 PMCID: PMC1223474 DOI: 10.1042/bj20021876] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2002] [Revised: 03/17/2003] [Accepted: 04/01/2003] [Indexed: 11/17/2022]
Abstract
Human cytosolic beta-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays beta-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (beta/alpha)(8)-barrel fold characteristic of family 1 beta-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val(168)-->Tyr, Phe(225)-->Ser, Tyr(308)-->Ala and Tyr(308)-->Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val(168)-->Tyr mutation did not affect K (m) on p -nitrophenyl ( p NP)-glycosides, but increased K (m) 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe(225)-->Ser and Tyr(308)-->Ala mutations, and, to a lesser degree, the Tyr(308)-->Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.
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Affiliation(s)
- Jean-Guy Berrin
- Institute of Food Research, Colney Lane, Norwich NR4 7UA, UK
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26
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Wang X, He X, Yang S, An X, Chang W, Liang D. Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102. J Bacteriol 2003; 185:4248-55. [PMID: 12837801 PMCID: PMC164863 DOI: 10.1128/jb.185.14.4248-4255.2003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The three-dimensional structure of a thermostable beta-glycosidase (Gly(Tn)) from the thermophilic eubacterium Thermus nonproteolyticus HG102 was determined at a resolution of 2.4 A. The core of the structure adopts the (betaalpha)(8) barrel fold. The sequence alignments and the positions of the two Glu residues in the active center indicate that Gly(Tn) belongs to the glycosyl hydrolases of retaining family 1. We have analyzed the structural features of Gly(Tn) related to the thermostability and compared its structure with those of other mesophilic glycosidases from plants, eubacteria, and hyperthermophilic enzymes from archaea. Several possible features contributing to the thermostability of Gly(Tn) were elucidated.
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Affiliation(s)
- Xinquan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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27
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Bismuto E, Febbraio F, Limongelli S, Briante R, Nucci R. Dynamic fluorescence studies of beta-glycosidase mutants from Sulfolobus solfataricus: effects of single mutations on protein thermostability. Proteins 2003; 51:10-20. [PMID: 12596260 DOI: 10.1002/prot.10317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Multiple sequence alignment on 73 proteins belonging to glycosyl hydrolase family 1 reveals the occurrence of a segment (83-124) in the enzyme sequences from hyperthermophilic archaea bacteria, which is absent in all the mesophilic members of the family. The alignment of the known three-dimensional structures of hyperthermophilic glycosidases with the known ones from mesophilic organisms shows a similar spatial organizations of beta-glycosidases except for this sequence segment whose structure is located on the external surface of each of four identical subunits, where it overlaps two alpha-helices. Site-directed mutagenesis substituting N97 or S101 with a cysteine residue in the sequence of beta-glycosidase from hyperthermophilic archaeon Sulfolobus solfataricus caused some changes in the structural and dynamic properties as observed by circular dichroism in far- and near-UV light, as well as by frequency domain fluorometry, with a simultaneous loss of thermostability. The results led us to hypothesize an important role of the sequence segment present only in hyperthermophilic beta-glycosidases, in the thermal adaptation of archaea beta-glycosidases. The thermostabilization mechanism could occur as a consequence of numerous favorable ionic interactions of the 83-124 sequence with the other part of protein matrix that becomes more rigid and less accessible to the insult of thermal-activated solvent molecules.
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Affiliation(s)
- Ettore Bismuto
- Dipartimento di Biochimica e Biofisica, Seconda Università di Napoli, Napoli, Italy.
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28
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Cobucci-Ponzano B, Moracci M, Di Lauro B, Ciaramella M, D'Avino R, Rossi M. Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization. Proteins 2002; 48:98-106. [PMID: 12012341 DOI: 10.1002/prot.10128] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Biochemical, crystallographic, and computational data support the hypothesis that electrostatic interactions are among the dominant forces in stabilizing hyperthermophilic proteins. The thermostable beta-glycosidase from the hyperthermophile Sulfolobus solfataricus (Ssbeta-gly) is an interesting model system for the study of protein adaptation to high temperatures. The largest ion-pair network of Ssbeta-gly is located at the tetrameric interface of the molecule; in this paper, key residues in this region were modified by site-directed mutagenesis and the stability of the mutants was analyzed by kinetics of thermal denaturation. All mutations produced faster enzyme inactivation, suggesting that the C-terminal ionic network prevents the dissociation into monomers, which is the limiting step in the mechanism of Ssbeta-gly inactivation. Moreover, the calculated reaction order showed that the mechanism of inactivation depends on the mutation introduced, suggesting that intermediates maintaining enzymatic activity are produced during the inactivation transition of some, but not all, mutants. Molecular models of each mutant allow us to rationalize the experimental evidence and give support to the current theories on the mechanism of ion pair stabilization in proteins from hyperthermophiles.
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29
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Berrin JG, McLauchlan WR, Needs P, Williamson G, Puigserver A, Kroon PA, Juge N. Functional expression of human liver cytosolic beta-glucosidase in Pichia pastoris. Insights into its role in the metabolism of dietary glucosides. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:249-58. [PMID: 11784319 DOI: 10.1046/j.0014-2956.2001.02641.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human tissues such as liver, small intestine, spleen and kidney contain a cytosolic beta-glucosidase (CBG) that hydrolyses various beta-d-glycosides, but whose physiological function is not known. Here, we describe the first heterologous expression of human CBG, a system that facilitated a detailed assessment of the enzyme specificity towards dietary glycosides. A full-length CBG cDNA (cbg-1) was cloned from a human liver cDNA library and expressed in the methylotrophic yeast Pichia pastoris at a secretion yield of approximately 10 mg x L-1. The recombinant CBG (reCBG) was purified from the supernatant using a single chromatography step and was shown to be similar to the native enzyme isolated from human liver in terms of physical properties and specific activity towards 4-nitrophenyl-beta-D-glucoside. Furthermore, the reCBG displayed a broad specificity with respect to the glycone moiety of various aryl-glycosides (beta-D-fucosides, alpha-L-arabinosides, beta-D-glucosides, beta-D-galactosides, beta-L-xylosides, beta-D-arabinosides), similar to the native enzyme. For the first time, we show that the human enzyme has significant activity towards many common dietary xenobiotics including glycosides of phytoestrogens, flavonoids, simple phenolics and cyanogens with higher apparent affinities (K(m)) and specificities (k(cat)/K(m)) for dietary xenobiotics than for other aryl-glycosides. These data indicate that human CBG hydrolyses a broad range of dietary glucosides and may play a critical role in xenobiotic metabolism.
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Affiliation(s)
- Jean-Guy Berrin
- Nutrition, Health and Consumer Sciences Division, Institute of Food Research, Norwich, UK
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30
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Zouhar J, Vévodová J, Marek J, Damborský J, Su XD, Brzobohatý B. Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1. PLANT PHYSIOLOGY 2001. [PMID: 11706179 DOI: 10.1104/pp.010712] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The maize (Zea mays) beta-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-A resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased K(m) of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in k(cat) was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation.
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Affiliation(s)
- J Zouhar
- Department of Functional Genomics and Proteomics, Faculty of Science, Masaryk University, Kotláská 2, CZ-61137 Brno, Czech Republic
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31
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Hall BG. Predicting evolutionary potential. I. Predicting the evolution of a lactose-PTS system in Escherichia coli. Mol Biol Evol 2001; 18:1389-400. [PMID: 11420377 DOI: 10.1093/oxfordjournals.molbev.a003923] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genomes contain not only information for current biological functions, but also information for potential novel functions that may allow the host to adapt to new environments. The field of experimental evolution studies that potential by selecting for novel functions and deducing the means by which the function evolved, but until now it has not attempted to predict the outcomes of such experiments. Here I present a model system that is being developed specifically to examine the issue of what kind of information is most useful in predicting how novel functions will evolve. The system is the evolution of a Lac-PTS transport system and a phospho-beta-galactosidase hydrolase system as a novel pathway for metabolism of lactose in Escherichia coli. Two kinds of information, sequence-based phylogenetic inference and biochemical activity, are considered as predictors of which E. coli genes will evolve the required new functions. Both biochemical data and phylogenetic inference predict that the cryptic celABC genes, which currently specify a PTS-beta-glucoside transport system, are most likely to evolve into a PTS-lactose transport system. Phylogenetic inference predicts that the bglA gene, which currently specifies a phospho-beta-glucosidase, is most likely to evolve into a phospho-beta-galactosidase. In contrast, biochemical data predict that the cryptic bglB gene, which also currently specifies a phospho-beta-glucosidase, is most likely to evolve into a phospho-beta-galactosidase.
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Affiliation(s)
- B G Hall
- Department of Biology, University of Rochester, New York 14625-0222, USA.
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32
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Affiliation(s)
- M Moracci
- Institute of Protein Biochemistry and Enzymology, CNR, 80125 Naples, Italy
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33
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Czjzek M, Cicek M, Zamboni V, Burmeister WP, Bevan DR, Henrissat B, Esen A. Crystal structure of a monocotyledon (maize ZMGlu1) beta-glucosidase and a model of its complex with p-nitrophenyl beta-D-thioglucoside. Biochem J 2001; 354:37-46. [PMID: 11171077 PMCID: PMC1221626 DOI: 10.1042/0264-6021:3540037] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The maize beta-glucosidase isoenzymes ZMGlu1 and ZMGlu2 hydrolyse the abundant natural substrate DIMBOAGlc (2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one), whose aglycone DIMBOA (2,4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) is the major defence chemical protecting seedlings and young plant parts against herbivores and other pests. The two isoenzymes hydrolyse DIMBOAGlc with similar kinetics but differ from each other and their sorghum homologues with respect to specificity towards other substrates. To gain insights into the mechanism of substrate (i.e. aglycone) specificity between the two maize isoenzymes and their sorghum homologues, ZMGlu1 was produced in Escherichia coli, purified, crystallized and its structure solved at 2.5 Angstrom resolution by X-ray crystallography. In addition, the complex of ZMGlu1 with the non-hydrolysable inhibitor p-nitrophenyl beta-D-thioglucoside was crystallized and, based on the partial electron density, a model for the inhibitor molecule within the active site is proposed. The inhibitor is located in a slot-like active site where its aromatic aglycone is held by stacking interactions with Trp-378. Whereas some of the atoms on the non-reducing end of the glucose moiety can be modelled on the basis of the electron density, most of the inhibitor atoms are highly disordered. This is attributed to the requirement of the enzyme to accommodate two different species, namely the substrate in its ground state and in its distorted conformation, for catalysis.
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Affiliation(s)
- M Czjzek
- Architecture et Fonction des Macromolecules Biologiques-AFMB-UMR 6098, CNRS and Universités d'Aix-Marseille I et II, 31 Chemin Joseph Aiguier, F13402 Marseille Cedex 20, France.
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34
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Arrizubieta MJ, Polaina J. Increased thermal resistance and modification of the catalytic properties of a beta-glucosidase by random mutagenesis and in vitro recombination. J Biol Chem 2000; 275:28843-8. [PMID: 10871610 DOI: 10.1074/jbc.m003036200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bglB gene from Paenibacillus polymyxa was subjected to random mutagenesis mediated by error prone polymerase chain reaction amplification and DNA shuffling. After this treatment, mutant variants of the encoded beta-glucosidase with enhanced thermal resistance were selected. We identified five amino acid substitutions at four different positions of the sequence that increased the resistance of the enzyme to heat denaturation. Four of the mutations, H62R, M319V, M319I, and M361I, did not change the kinetic parameters of the enzyme. However, mutant N223Y, which caused only a marginal increase in thermoresistance, showed an 8-fold decrease in K(m). Copies of the bglB gene carrying each one of the individual mutations were recombined in vitro by DNA shuffling. As a result, we obtained an enzyme that simultaneously exhibited a 20-fold increase in heat resistance and an 8-fold increase in the catalytic efficiency. The structural basis of the properties conferred by the mutations was analyzed using homology-based structural models. The four mutations causing a more pronounced effect on thermoresistance were located in loops, on the periphery of the (alpha/beta)(8) barrel that conforms the structure of the protein. Mutation N223Y, which modifies the catalytic properties of the enzyme, was on one of the barrel beta-strands that shape the active center.
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Affiliation(s)
- M J Arrizubieta
- Instituto de Agroquimica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientifícas, Apdo. 73, E46100-Burjassot, Valencia, Spain
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35
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Abstract
Enzymatic hydrolysis of glycosides can occur by one of two elementary mechanisms identified by the stereochemical outcome of the reaction, inversion or retention. The key active-site residues involved are a pair of carboxylic acids in each case, and strategies for their identification and for probing the details of their roles in catalysis have been developed through detailed kinetic analysis of mutants. Similarly the roles of other active-site residues have also been probed this way, and mutants have been developed that trap intermediates in catalysis, allowing the determination of the three-dimensional structures of several such key species. By manipulating the locations or even the presence of these carboxyl side chains in the active site, the mechanisms of several glycosidases have been completely changed, and this has allowed the development of "glycosynthases," mutant glycosidases that are capable of synthesizing oligosaccharides but unable to degrade them. Surprisingly little progress has been made on altering specificities through mutagenesis, although recent results suggest that gene shuffling coupled with effective screens will provide the most effective approach.
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Affiliation(s)
- H D Ly
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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36
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Schulte D, Hengstenberg W. Engineering the active center of the 6-phospho-beta-galactosidase from Lactococcus lactis. PROTEIN ENGINEERING 2000; 13:515-8. [PMID: 10906347 DOI: 10.1093/protein/13.7.515] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Several amino acids in the active center of the 6-phospho-beta-galactosidase from Lactococcus lactis were replaced by the corresponding residues in homologous enzymes of glycosidase family 1 with different specificities. Three mutants, W429A, K435V/Y437F and S428D/ K435V/Y437F, were constructed. W429A was found to have an improved specificity for glucosides compared with the wild-type, consistent with the theory that the amino acid at this position is relevant for the distinction between galactosides and glucosides. The k(cat)/K(m) for o-nitrophenyl-beta-D-glucose-6-phosphate is 8-fold higher than for o-nitrophenyl-beta-D-galactose-6-phosphate which is the preferred substrate of the wild-type enzyme. This suggests that new hydrogen bonds are formed in the mutant between the active site residues, presumably Gln19 or Trp421 and the C-4 hydroxyl group. The two other mutants with the exchanges in the phosphate-binding loop were tested for their ability to bind phosphorylated substrates. The triple mutant is inactive. The double mutant has a dramatically decreased ability to bind o-nitrophenyl-beta-D-galactose-6-phosphate whereas the interaction with o-nitrophenyl-beta-D-galactose is barely altered. This result shows that the 6-phospho-beta-galactosidase and the related cyanogenic beta-glucosidase from Trifolium repens have different recognition mechanisms for substrates although the structures of the active sites are highly conserved.
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Affiliation(s)
- D Schulte
- Arbeitsgruppe Physiologie der Mikroorganismen, Department of Biology, Ruhr-Universität Bochum, D- 44780 Bochum, Germany
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37
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Cicek M, Blanchard D, Bevan DR, Esen A. The aglycone specificity-determining sites are different in 2, 4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA)-glucosidase (Maize beta -glucosidase) and dhurrinase (Sorghum beta -glucosidase). J Biol Chem 2000; 275:20002-11. [PMID: 10748038 DOI: 10.1074/jbc.m001609200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The maize beta-glucosidase isozyme Glu1 hydrolyzes a broad spectrum of substrates in addition to its natural substrate DIMBOAGlc (2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-on e), whereas the sorghum beta-glucosidase isozyme Dhr1 hydrolyzes exclusively its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-d-glucose). To study the mechanism of substrate specificity further, eight chimeric beta-glucosidases were constructed by replacing peptide sequences within the C-terminal region of Glu1 with the homologous peptide sequences of Dhr1 or vice versa, where the two enzymes differ by 4 to 22 amino acid substitutions, depending on the length of the swapped regions. Five Glu1/Dhr1 chimeras hydrolyzed substrates that are hydrolyzed by both parental enzymes, including dhurrin, which is not hydrolyzed by Glu1. In contrast, three Dhr1/Glu1 chimeras hydrolyzed only dhurrin but with lower catalytic efficiency than Dhr1. Additional domain-swapping within the C-terminal domain of Glu1 showed that replacing the peptide (466)FAGFTERY(473) of Glu1 with the homologous peptide (462)SSGYTERF(469) of Dhr1 or replacing the peptide (481)NNNCTRYMKE(490) in Glu1 with the homologous peptide (477)ENGCERTMKR(486) of Dhr1 was sufficient to confer to Glu1 the ability to hydrolyze dhurrin. Data from various reciprocal chimeras, sequence comparisons, and homology modeling suggest that the Dhr1-specific Ser-462-Ser-463 and Phe-469 play a key role in dhurrin hydrolysis. Similar data suggest that DIMBOAGlc hydrolysis determinants are not located within the extreme 47-amino acid-long C-terminal domain of Glu1.
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Affiliation(s)
- M Cicek
- Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0406, USA
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38
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Hakulinen N, Paavilainen S, Korpela T, Rouvinen J. The crystal structure of beta-glucosidase from Bacillus circulans sp. alkalophilus: ability to form long polymeric assemblies. J Struct Biol 2000; 129:69-79. [PMID: 10675298 DOI: 10.1006/jsbi.1999.4206] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Family 1 of glycosyl hydrolases is a large and biologically important group of enzymes. A new three-dimensional structure of this family, beta-glucosidase from Bacillus circulans sp. alkalophilus is reported here. This is the first structure of beta-glucosidase from an alkaliphilic organism. The model was determined by the molecular replacement method and refined to a resolution of 2.7 A. The quaternary structure of B. circulans sp. alkalophilus beta-glucosidase is an octamer and subunits of the octamer show a similar (beta/alpha)(8) barrel fold to that previously reported for other family 1 enzymes. The crystal structure suggested that Cys169 in the active site is substituted. The Cys169 is located near the putative acid/base catalyst Glu166 and it may contribute to the high pH optimum of the enzyme. The crystal structure also revealed that the asymmetric unit contains two octamers which have a clear binding interaction with each other. The ability of the octamers to link with each other suggested that beta-glucosidase from Bacillus circulans sp. alkalophilus is able to form long polymeric assemblies, at least in the crystalline state.
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Affiliation(s)
- N Hakulinen
- Department of Chemistry, University of Joensuu, Joensuu, 80101, Finland
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39
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Callahan JW. Molecular basis of GM1 gangliosidosis and Morquio disease, type B. Structure-function studies of lysosomal beta-galactosidase and the non-lysosomal beta-galactosidase-like protein. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1455:85-103. [PMID: 10571006 DOI: 10.1016/s0925-4439(99)00075-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
GM1 gangliosidosis and Morquio B disease are distinct disorders both clinically and biochemically yet they arise from the same beta-galactosidase enzyme deficiency. On the other hand, galactosialidosis and sialidosis share common clinical and biochemical features, yet they arise from two separate enzyme deficiencies, namely, protective protein/cathepsin A and neuraminidase, respectively. However distinct, in practice these disorders overlap both clinically and biochemically so that easy discrimination between them is sometimes difficult. The principle reason for this may be found in the fact that these three enzymes form a unique complex in lysosomes that is required for their stability and posttranslational processing. In this review, I focus mainly on the primary and secondary beta-galactosidase deficiency states and offer some hypotheses to account for differences between GM1 gangliosidosis and Morquio B disease.
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Affiliation(s)
- J W Callahan
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, ON, Canada.
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40
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41
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Chi YI, Martinez-Cruz LA, Jancarik J, Swanson RV, Robertson DE, Kim SH. Crystal structure of the beta-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability. FEBS Lett 1999; 445:375-83. [PMID: 10094493 DOI: 10.1016/s0014-5793(99)00090-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The glycosyl hydrolases are an important group of enzymes that are responsible for cleaving a range of biologically significant carbohydrate compounds. Structural information on these enzymes has provided useful information on their molecular basis for the functional variations, while the characterization of the structural features that account for the high thermostability of proteins is of great scientific and biotechnological interest. To these ends we have determined the crystal structure of the beta-glycosidase from a hyperthermophilic archeon Thermosphaera aggregans. The structure is a (beta/alpha)8 barrel (TIM-barrel), as seen in other glycosyl hydrolase family 1 members, and forms a tetramer. Inspection of the active site and the surrounding area reveals two catalytic glutamate residues consistent with the retaining mechanism and the surrounding polar and aromatic residues consistent with a monosaccharide binding site. Comparison of this structure with its mesophilic counterparts implicates a variety of structural features that could contribute to the thermostability. These include an increased number of surface ion pairs, an increased number of internal water molecules and a decreased surface area upon forming an oligomeric quaternary structure.
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Affiliation(s)
- Y I Chi
- Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA
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42
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Varghese JN, Hrmova M, Fincher GB. Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase. Structure 1999; 7:179-90. [PMID: 10368285 DOI: 10.1016/s0969-2126(99)80024-0] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cell walls of the starchy endosperm and young vegetative tissues of barley (Hordeum vulgare) contain high levels of (1-->3,1-->4)-beta-D-glucans. The (1-->3,1-->4)-beta-D-glucans are hydrolysed during wall degradation in germinated grain and during wall loosening in elongating coleoptiles. These key processes of plant development are mediated by several polysaccharide endohydrolases and exohydrolases. RESULTS . The three-dimensional structure of barley beta-D-glucan exohydrolase isoenzyme ExoI has been determined by X-ray crystallography. This is the first reported structure of a family 3 glycosyl hydrolase. The enzyme is a two-domain, globular protein of 605 amino acid residues and is N-glycosylated at three sites. The first 357 residues constitute an (alpha/beta)8 TIM-barrel domain. The second domain consists of residues 374-559 arranged in a six-stranded beta sandwich, which contains a beta sheet of five parallel beta strands and one antiparallel beta strand, with three alpha helices on either side of the sheet. A glucose moiety is observed in a pocket at the interface of the two domains, where Asp285 and Glu491 are believed to be involved in catalysis. CONCLUSIONS The pocket at the interface of the two domains is probably the active site of the enzyme. Because amino acid residues that line this active-site pocket arise from both domains, activity could be regulated through the spatial disposition of the domains. Furthermore, there are sites on the second domain that may bind carbohydrate, as suggested by previously published kinetic data indicating that, in addition to the catalytic site, the enzyme has a second binding site specific for (1-->3, 1-->4)-beta-D-glucans.
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Affiliation(s)
- J N Varghese
- Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria 3052 Australia.
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Dion M, Fourage L, Hallet JN, Colas B. Cloning and expression of a beta-glycosidase gene from Thermus thermophilus. Sequence and biochemical characterization of the encoded enzyme. Glycoconj J 1999; 16:27-37. [PMID: 10580648 DOI: 10.1023/a:1006997602727] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A 3.2 kilobase pair DNA fragment from Thermus thermophilus HB27 coding for a beta-galactosidase activity was cloned and sequenced. A gene and a truncated open reading frame orf1 encoding respectively a beta-glycosidase (ttbeta-gly) and probably a sugar permease were located directly adjacent to each other. The deduced aminoacid sequence of the enzyme Ttbeta-gly showed strong identity with those of beta-glycosidases belonging to the glycosyl hydrolase family 1. The enzyme was overexpressed in Escherichia coli and was purified by a two-step purification procedure. The recombinant enzyme is monomeric with a molecular mass of 49-kDa. It catalyzes the hydrolysis of beta-D-galactoside, beta-D-glucoside and beta-D-fucoside derivatives. However, the kcat/Km ratio is much higher for p-nitrophenyl-beta-D-glucoside and p-nitrophenyl-beta-D-fucoside than for p-nitrophenyl-beta-D-galactoside. The specificity towards linkage positions of the disaccharides tested decreased in the following order: beta1-3 (100%) > beta1-2 (71%) > beta1-4 (40%) > beta1-6 (10%). Ttbeta-gly is a thermostable enzyme displaying an optimum temperature of 88 degrees C and a half life of 10 min at 90 degrees C. It performs transglycosylation reactions at high temperature with a yield exceeding 63% for transfucosylation reactions. On the basis of this work, the enzyme appears to be an attractive tool in the synthesis of fucosyl adducts and fucosyl sugars.
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Affiliation(s)
- M Dion
- Unité de Recherche sur la Biocatalyse, Faculté des Sciences et Techniques, Université de Nantes, France
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44
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D'Auria S, Moracci M, Febbraio F, Tanfani F, Nucci R, Rossi M. Structure-function studies on beta-glycosidase from Sulfolobus solfataricus. Molecular bases of thermostability. Biochimie 1998; 80:949-57. [PMID: 9893955 DOI: 10.1016/s0300-9084(00)88892-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
beta-Glycosidase from the extreme thermophilic archaeon Sulfolobus solfataricus is a thermostable tetrameric protein with a molecular mass of 240 kDa which is stable in the presence of detergents and has a maximal activity above 95 degrees C. An understanding of the structure-function relationship of the enzyme under different chemical-physical conditions is of fundamental importance for both theoretical and application purposes. In this paper we report the effect of basic pH values on the structural stability of this enzyme. The structure of the enzyme was studied at pH 10 and in the temperature range 25-97.5 degrees C using circular dichroism, Fourier-transform infrared and fluorescence spectroscopy. The spectroscopic data indicated that the enzyme stability was strongly affected by pH 10 suggesting that the destabilization of the protein structure is correlated with the perturbation of ionic interactions present in the native protein at neutral pHs. These experiments give support to the observation derived from the 3D-structure, that large ion pair networks on the surface stabilize Sulfolobus solfataricus beta-glycosidase.
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Affiliation(s)
- S D'Auria
- Istituto di Biochimica delle Proteine ed Enzimologia, Consiglio Nazionale delle Ricerche, Naples, Italy
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45
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Thompson J, Pikis A, Ruvinov SB, Henrissat B, Yamamoto H, Sekiguchi J. The gene glvA of Bacillus subtilis 168 encodes a metal-requiring, NAD(H)-dependent 6-phospho-alpha-glucosidase. Assignment to family 4 of the glycosylhydrolase superfamily. J Biol Chem 1998; 273:27347-56. [PMID: 9765262 DOI: 10.1074/jbc.273.42.27347] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene glvA (formerly glv-1) from Bacillus subtilis has been cloned and expressed in Escherichia coli. The purified protein GlvA (449 residues, Mr = 50,513) is a unique 6-phosphoryl-O-alpha-D-glucopyranosyl:phosphoglucohydrolase (6-phospho-alpha-glucosidase) that requires both NAD(H) and divalent metal (Mn2+, Fe2+, Co2+, or Ni2+) for activity. 6-Phospho-alpha-glucosidase (EC 3.2.1.122) from B. subtilis cross-reacts with polyclonal antibody to maltose 6-phosphate hydrolase from Fusobacterium mortiferum, and the two proteins exhibit amino acid sequence identity of 73%. Estimates for the Mr of GlvA determined by SDS-polyacrylamide gel electrophoresis (51,000) and electrospray-mass spectroscopy (50,510) were in excellent agreement with the molecular weight of 50,513 deduced from the amino acid sequence. The sequence of the first 37 residues from the N terminus determined by automated analysis agreed precisely with that predicted by translation of glvA. The chromogenic and fluorogenic substrates, p-nitrophenyl-alpha-D-glucopyranoside 6-phosphate and 4-methylumbelliferyl-alpha-D-glucopyranoside 6-phosphate were used for the discontinuous assay and in situ detection of enzyme activity, respectively. Site-directed mutagenesis shows that three acidic residues, Asp41, Glu111, and Glu359, are required for GlvA activity. Asp41 is located at the C terminus of a betaalphabeta fold that may constitute the dinucleotide binding domain of the protein. Glu111 and Glu359 may function as the catalytic acid (proton donor) and nucleophile (base), respectively, during hydrolysis of 6-phospho-alpha-glucoside substrates including maltose 6-phosphate and trehalose 6-phosphate. In metal-free buffer, GlvA exists as an inactive dimer, but in the presence of Mn2+ ion, these species associate to form the NAD(H)-dependent catalytically active tetramer. By comparative sequence alignment with its homologs, the novel 6-phospho-alpha-glucosidase from B. subtilis can be assigned to the nine-member family 4 of the glycosylhydrolase superfamily.
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Affiliation(s)
- J Thompson
- Microbial Biochemistry and Genetics Unit, Oral Infection and Immunity Branch, NIDR, National Institutes of Health, Bethesda, Maryland 20892, USA.
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46
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Vonrhein C, Bönisch H, Schäfer G, Schulz GE. The structure of a trimeric archaeal adenylate kinase. J Mol Biol 1998; 282:167-79. [PMID: 9733648 DOI: 10.1006/jmbi.1998.2003] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The adenylate kinase from the hyperthermophilic archaean species Sulfolobus acidocaldarius has been cloned, expressed in Escherichia coli, purified and crystallized. The crystal structure was elucidated by multiple isomorphous replacement and non-crystallographic density averaging. The structure was refined at 2.6 A (1 A=0.1 nm) resolution. The enzyme is trimeric, in contrast to previous solution measurements that suggested a dimeric structure, and in contrast to the vast majority of adenylate kinases, which are monomeric. In large parts of each subunit the chain fold resembles the known enzyme structure from eubacteria and eukaryotes although the sequence homology is negligible. Since the asymmetric unit contains two trimers with and without bound AMP at the AMP sites and with an ADP at one of the six ATP sites, the analysis shows the enzyme in several states. The conformational differences between these states resemble those of other adenylate kinases. Because of sequence homology, the structure presented provides a good model for the methanococcal adenylate kinases.
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Affiliation(s)
- C Vonrhein
- Institut für Organische Chemie und Biochemie, Albertstr. 21, Freiburg im Breisgau, D-79104, Germany
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47
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Lawson SL, Warren RA, Withers SG. Mechanistic consequences of replacing the active-site nucleophile Glu-358 in Agrobacterium sp. beta-glucosidase with a cysteine residue. Biochem J 1998; 330 ( Pt 1):203-9. [PMID: 9461511 PMCID: PMC1219128 DOI: 10.1042/bj3300203] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Retaining glycosidases achieve the hydrolysis of glycosidic bonds through the assistance of two key active-site carboxyls. One carboxyl functions as a nucleophile/leaving group, and the other acts as the acid-base catalyst. It has been suggested that a cysteine residue could fulfil the role of the active site nucleophile [Hardy and Poteete (1991) Biochemistry 30, 9457-9463]. To test the validity of this proposal, a kinetic evaluation was conducted on the active-site nucleophile cysteine mutant (Glu-358-->Cys) of the retaining beta-glucosidase from Agrobacterium sp. The Glu-358-->Cys mutant was able to complete the first step (glycosylation) of the enzymic mechanism, forming a covalent glycosyl-enzyme intermediate, but the rate constant for this step was decreased to 1/10(6) of that of the native enzyme. The subsequent hydrolysis (deglycosylation) step was also severely affected by the replacement of Glu-358 with a cysteine residue, with the rate constant being depressed to 1/10(7) or less. Thus Cys-358 functions inefficiently in both the capacity of catalytic nucleophile and leaving group. On the basis of these results it seems unlikely that the role of the active-site nucleophile in retaining glycosidases could successfully be filled by a cysteine residue.
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Affiliation(s)
- S L Lawson
- Protein Engineering Network of Centres of Excellence and the Departments of Chemistry and Microbiology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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48
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Sanz-Aparicio J, Hermoso JA, Martínez-Ripoll M, Lequerica JL, Polaina J. Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases. J Mol Biol 1998; 275:491-502. [PMID: 9466926 DOI: 10.1006/jmbi.1997.1467] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Family 1 glycosyl hydrolases are a very relevant group of enzymes because of the diversity of biological roles in which they are involved, and their generalized occurrence in all sorts of living organisms. The biological plasticity of these enzymes is a consequence of the variety of beta-glycosidic substrates that they can hydrolyze: disaccharides such as cellobiose and lactose, phosphorylated disaccharides, cyanogenic glycosides, etc. The crystal structure of BglA, a member of the family, has been determined in the native state and complexed with gluconate ligand, at 2.4 A and 2.3 A resolution, respectively. The subunits of the octameric enzyme display the (alpha/beta)8 barrel structural fold previously reported for other family 1 enzymes. However, significant structural differences have been encountered in the loops surrounding the active-center cavity. These differences make a wide and extended cavity in BglA, which seems to be able to accommodate substrates longer than cellobiose, its natural substrate. Furthermore, a third sub-site is encountered, which might have some connection with the transglycosylating activity associated to this enzyme and its certain activity against beta-1,4 oligosaccharides composed of more than two units of glucose. The particular geometry of the cavity which contains the active center of BglA must therefore account for both, hydrolytic and transglycosylating activities. A potent and well known inhibitor of different glycosidases, D-glucono-1,5-lactone, was used in an attempt to define interactions of the substrate with specific protein residues. Although the lactone has transformed into gluconate under crystallizing conditions, the open species still binds the enzyme, the conformation of its chain mimicking the true inhibitor. From the analysis of the enzyme-ligand hydrogen bonding interactions, a detailed picture of the active center can be drawn, for a family 1 enzyme. In this way, Gln20, His121, Tyr296, Glu405 and Trp406 are identified as determinant residues in the recognition of the substrate. In particular, two bidentate hydrogen bonds made by Gln20 and Glu405, could conform the structural explanation for the ability of most members of the family for displaying both, glucosidase and galactosidase activity.
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Affiliation(s)
- J Sanz-Aparicio
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
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49
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Benner SA, Cannarozzi G, Gerloff D, Turcotte M, Chelvanayagam G. Bona Fide Predictions of Protein Secondary Structure Using Transparent Analyses of Multiple Sequence Alignments. Chem Rev 1997; 97:2725-2844. [PMID: 11851479 DOI: 10.1021/cr940469a] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven A. Benner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200
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50
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Devulapalle KS, Goodman SD, Gao Q, Hemsley A, Mooser G. Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci. Protein Sci 1997; 6:2489-93. [PMID: 9416598 PMCID: PMC2143619 DOI: 10.1002/pro.5560061201] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mutans streptococci glucosyltransferases catalyze glucosyl transfer from sucrose to a glucan chain. We previously identified an aspartyl residue that participates in stabilizing the glucosyl transition state. The sequence surrounding the aspartate was found to have substantial sequence similarity with members of alpha-amylase family. Because little is known of the protein structure beyond the amino acid sequence, we used a knowledge-based interactive algorithm, MACAW, which provided significant level of homology with alpha-amylases and glucosyltransferase from Streptococcus downei gtfI (GTF). The significance of GTF similarity is underlined by GTF/alpha-amylase residues conserved in all but one alpha-amylase invariant residues. Site-directed mutagenesis of the three GTF catalytic residues are homologous with the alpha-amylase catalytic triad. The glucosyltransferases are members of the 4/7-superfamily that have a (beta/alpha)8-barrel structure and belong to family 13 of the glycohydralases.
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Affiliation(s)
- K S Devulapalle
- Department of Basic Sciences, School of Dentistry, University of Southern California, Los Angeles 90089-0641, USA
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