1
|
Nakamura S, Kurata R, Miyazaki T. Structural insights into α-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae. FEBS J 2024; 291:3267-3282. [PMID: 38661728 DOI: 10.1111/febs.17139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/07/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Glycoside hydrolase family 97 (GH97) comprises enzymes like anomer-inverting α-glucoside hydrolases (i.e., glucoamylase) and anomer-retaining α-galactosidases. In a soil bacterium, Flavobacterium johnsoniae, we previously identified a GH97 enzyme (FjGH97A) within the branched dextran utilization locus. It functions as an α-glucoside hydrolase, targeting α-(1→6)-glucosidic linkages in dextran and isomaltooligosaccharides (i.e., glucodextranase). FjGH97A exhibits a preference for α-(1→6)-glucoside linkages over α-(1→4)-linkages, while Bacteroides thetaiotaomicron glucoamylase SusB (with 69% sequence identity), which is involved in the starch utilization system, exhibits the highest specificity for α-(1→4)-glucosidic linkages. Here, we examined the crystal structures of FjGH97A in complexes with glucose, panose, or isomaltotriose, and analyzed the substrate preferences of its mutants to identify the amino acid residues that determine the substrate specificity for α-(1→4)- and α-(1→6)-glucosidic linkages. The overall structure of FjGH97A resembles other GH97 enzymes, with conserved catalytic residues similar to anomer-inverting GH97 enzymes. A comparison of active sites between FjGH97A and SusB revealed differences in amino acid residues at subsites +1 and +2 (specifically Ala195 and Ile378 in FjGH97A). Among the three mutants (A195S, I378F, and A195S-I378F), A195S and A195S-I378F exhibited increased activity toward α-(1→4)-glucoside bonds compared to α-(1→6)-glucoside bonds. This suggests that Ala195, located on the Gly184-Thr203 loop (named loop-N) conserved within the GH97 subgroup, including FjGH97A and SusB, holds significance in determining linkage specificity. The conservation of alanine in the active site of the GH97 enzymes, within the same gene cluster as the putative dextranase, indicates its crucial role in determining the specificity for α-(1→6)-glucoside linkage.
Collapse
Affiliation(s)
- Shuntaro Nakamura
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Japan
| |
Collapse
|
2
|
Mendonça APS, Dos Reis KL, Barbosa-Tessmann IP. Aspergillus clavatus UEM 04: An efficient producer of glucoamylase and α-amylase able to hydrolyze gelatinized and raw starch. Int J Biol Macromol 2023; 249:125890. [PMID: 37479205 DOI: 10.1016/j.ijbiomac.2023.125890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/04/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
The best amylolytic activity production by Aspergillus clavatus UEM 04 occurred in submersed culture, with starch, for 72 h, at 25 °C, and 100 rpm. Exclusion chromatography partially purified two enzymes, which ran as unique bands in SDS-PAGE with approximately 84 kDa. LC-MS/MS identified a glucoamylase (GH15) and an α-amylase (GH13_1) as the predominant proteins and other co-purified proteins. Zn2+, Cu2+, and Mn2+ activated the glucoamylase, and SDS, Zn2+, Fe3+, and Cu2+ inhibited the α-amylase. The α-amylase optimum pH was 6.5. The optimal temperatures for the glucoamylase and α-amylase were 50 °C and 40 °C, and the Tm was 53.1 °C and 56.3 °C, respectively. Both enzymes remained almost fully active for 28-32 h at 40 °C, but the α-amylase thermal stability was calcium-dependent. Furthermore, the glucoamylase and α-amylase KM for starch were 2.95 and 1.0 mg/mL, respectively. Still, the Vmax was 0.28 μmol/min of released glucose for glucoamylase and 0.1 mg/min of consumed starch for α-amylase. Moreover, the glucoamylase showed greater affinity for amylopectin and α-amylase for maltodextrin. Additionally, both enzymes efficiently degraded raw starch. At last, glucose was the main product of glucoamylase, and α-amylase produced mainly maltose from gelatinized soluble starch hydrolysis.
Collapse
Affiliation(s)
- Ana Paula Silva Mendonça
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Karina Lima Dos Reis
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Ione Parra Barbosa-Tessmann
- Biological Sciences Center, Department of Biochemistry, Universidade Estadual de Maringá, Maringá, PR, Brazil.
| |
Collapse
|
3
|
OGAWA S, KUNO S, TOYOKUNI T. Design and synthesis of biologically active carbaglycosylamines: From glycosidase inhibitors to pharmacological chaperones. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:336-360. [PMID: 35908956 PMCID: PMC9363598 DOI: 10.2183/pjab.98.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
For over 50 years, our group has been involved in synthetic studies on biologically active cyclitols including carbasugars. Among a variety of compounds synthesized, this review focuses on carbaglycosylamine glycosidase inhibitors, highlighting the following: (1) the naturally occurring N-linked carbaoligosaccharide α-amylase inhibitor acarbose and related compounds; (2) the novel synthetic β-glycosidase inhibitors, 1'-epi-acarviosin and its 6-hydroxy analogue as well as β-valienaminylceramide and its 4'-epimer; (3) the discovery of the β-glycosidase inhibitors with chaperone activity, N-octyl-β-valienamine (NOV) and its 4-epimer (NOEV); and (4) the recent development of the potential pharmacological chaperone N-alkyl-conduramine F-4 derivatives.
Collapse
Affiliation(s)
- Seiichiro OGAWA
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, Japan
| | | | - Tatsushi TOYOKUNI
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, Japan
| |
Collapse
|
4
|
Characterization of SdGA, a cold-adapted glucoamylase from Saccharophagus degradans. ACTA ACUST UNITED AC 2021; 30:e00625. [PMID: 34041001 PMCID: PMC8141877 DOI: 10.1016/j.btre.2021.e00625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022]
Abstract
We investigated the structural and functional properties of SdGA, a glucoamylase (GA) from Saccharophagus degradans, a marine bacterium which degrades different complex polysaccharides at high rate. SdGA is composed mainly by a N-terminal GH15_N domain linked to a C-terminal catalytic domain (CD) found in the GH15 family of glycosylhydrolases with an overall structure similar to other bacterial GAs. The protein was expressed in Escherichia coli cells, purified and its biochemical properties were investigated. Although SdGA has a maximum activity at 39 °C and pH 6.0, it also shows high activity in a wide range, from low to mild temperatures, like cold-adapted enzymes. Furthermore, SdGA has a higher content of flexible residues and a larger CD due to various amino acid insertions compared to other thermostable GAs. We propose that this novel SdGA, is a cold-adapted enzyme that might be suitable for use in different industrial processes that require enzymes which act at low or medium temperatures.
Collapse
|
5
|
Lago MC, Dos Santos FC, Bueno PSA, de Oliveira MAS, Barbosa-Tessmann IP. The glucoamylase from Aspergillus wentii: Purification and characterization. J Basic Microbiol 2021; 61:443-458. [PMID: 33783000 DOI: 10.1002/jobm.202000595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/11/2021] [Accepted: 03/01/2021] [Indexed: 11/10/2022]
Abstract
This study describes for the first time the purification and characterization of a glucoamylase from Aspergillus wentii (strain PG18), a species of the Aspergillus genus Cremei section. Maximum enzyme production (∼3.5 U/ml) was obtained in submerged culture (72 h) with starch as the carbon source, at 25°C, and with orbital agitation (100 rpm). The enzyme was purified with one-step molecular exclusion chromatography. The 86 kDa purified enzyme hydrolyzed starch in a zymogram and had activity against p-nitrophenyl α- d-glucopyranoside. The optimal enzyme pH and temperature were 5.0 and 60°C (at pH 5.0), respectively. The Tm of the purified enzyme was 60°C, at pH 7.0. The purified glucoamylase had a KM for starch of 1.4 mg/ml and a Vmax of 0.057 mg/min of hydrolyzed starch. Molybdenum activated the purified enzyme, and sodium dodecyl sulfate inhibited it. A thin layer chromatography analysis revealed glucose as the enzyme's main starch hydrolysis product. An enzyme's peptide sequence was obtained by mass spectrometry and used to retrieve a glucoamylase within the annotated genome of A. wentii v1.0. An in silico structural model revealed a N-terminal glycosyl hydrolases family 15 (GH15) domain, which is ligated by a linker to a C-terminal carbohydrate-binding module (CBM) from the CBM20 family.
Collapse
Affiliation(s)
- Munira C Lago
- Department of Biochemistry, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Fabiane C Dos Santos
- Department of Biochemistry, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Paulo S A Bueno
- Department of Biochemistry, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Marco A S de Oliveira
- Department of Biochemistry, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | | |
Collapse
|
6
|
Schmidt A, Shvetsov A, Soboleva E, Kil Y, Sergeev V, Surzhik M. Thermostability improvement of Aspergillus awamori glucoamylase via directed evolution of its gene located on episomal expression vector in Pichia pastoris cells. Protein Eng Des Sel 2019; 32:251-259. [DOI: 10.1093/protein/gzz048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/21/2019] [Accepted: 11/30/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractNovel thermostable variants of glucoamylase (GA) from filamentous fungus Aspergillus awamori X100 were constructed using the directed evolution approach based on random mutagenesis by error-prone PCR of the catalytic domain region of glucoamylase gene located on a new episomal expression vector pPEHα in Pichia pastoris cells. Out of 3000 yeast transformants screened, six new thermostable GA variants with amino acid substitutions Val301Asp, Thr390Ala, Thr390Ala/Ser436Pro, Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu were identified and studied. To estimate the effect of each substitution in the double mutants, we have constructed the relevant single mutants of GA by site-directed mutagenesis and analyzed their thermal properties. Results of the analysis showed that only Ile82Phe and Ser8Arg substitutions by themselves increased enzyme thermostability. While the substitutions Leu7Met, Asn9His and Gln338Leu decreased the thermal stability of GA, the synergistic effect of double mutant variants Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu resulted in significant thermostability improvement as compared to the wild type GA. Thr390Ala and Thr390Ala/Ser436Pro mutant variants revealed the highest thermostability with free activation energy changes ΔΔG of 2.99 and 3.1 kJ/mol at 80°C, respectively.
Collapse
Affiliation(s)
- Alexander Schmidt
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- BioMedical Technology Department, Kurchatov Institute, Akademika Kurchatova square 1, Postal Code 123182, Moscow, Russia
| | - Alexey Shvetsov
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- BioMedical Technology Department, Kurchatov Institute, Akademika Kurchatova square 1, Postal Code 123182, Moscow, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Elena Soboleva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Yury Kil
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
| | - Vladimir Sergeev
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great Saint-Petersburg Polytechnic University, Polytechnicheskaya 29, Postal Code 195251, St. Petersburg, Russia
| | - Marina Surzhik
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Centre “Kurchatov Institute”, Orlova Roscha 1, Postal Code 188300, Gatchina, Russia
| |
Collapse
|
7
|
Roth C, Moroz OV, Ariza A, Skov LK, Ayabe K, Davies GJ, Wilson KS. Structural insight into industrially relevant glucoamylases: flexible positions of starch-binding domains. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:463-470. [PMID: 29717717 DOI: 10.1107/s2059798318004989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022]
Abstract
Glucoamylases are one of the most important classes of enzymes in the industrial degradation of starch biomass. They consist of a catalytic domain and a carbohydrate-binding domain (CBM), with the latter being important for the interaction with the polymeric substrate. Whereas the catalytic mechanisms and structures of the individual domains are well known, the spatial arrangement of the domains with respect to each other and its influence on activity are not fully understood. Here, the structures of three industrially used fungal glucoamylases, two of which are full length, have been crystallized and determined. It is shown for the first time that the relative orientation between the CBM and the catalytic domain is flexible, as they can adopt different orientations independently of ligand binding, suggesting a role as an anchor to increase the contact time and the relative concentration of substrate near the active site. The flexibility in the orientations of the two domains presented a considerable challenge for the crystallization of the enzymes.
Collapse
Affiliation(s)
- Christian Roth
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Olga V Moroz
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Antonio Ariza
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Lars K Skov
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark
| | | | - Gideon J Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Keith S Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| |
Collapse
|
8
|
Nierengarten JF, Schneider JP, Trinh TMN, Joosten A, Holler M, Lepage ML, Bodlenner A, García-Moreno MI, Ortiz Mellet C, Compain P. Giant Glycosidase Inhibitors: First- and Second-Generation Fullerodendrimers with a Dense Iminosugar Shell. Chemistry 2018; 24:2483-2492. [DOI: 10.1002/chem.201705600] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Jean-François Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Jérémy P. Schneider
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Thi Minh Nguyet Trinh
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Antoine Joosten
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Michel Holler
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Mathieu L. Lepage
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - Anne Bodlenner
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| | - M. Isabel García-Moreno
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; Profesor García González 1 41012 Sevilla Spain
| | - Carmen Ortiz Mellet
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; Profesor García González 1 41012 Sevilla Spain
| | - Philippe Compain
- Laboratoire de Synthèse Organique et Molécules Bioactives; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg Cedex 2 France
| |
Collapse
|
9
|
Xian L, Feng JX. Purification and biochemical characterization of a novel mesophilic glucoamylase from Aspergillus tritici WZ99. Int J Biol Macromol 2017; 107:1122-1130. [PMID: 28951303 DOI: 10.1016/j.ijbiomac.2017.09.095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 11/17/2022]
Abstract
Glucoamylase, cleaving the nonreducing end of starch releasing glucose, is an important enzyme in starch processing. The optimal temperature for industrial glucoamylase activity is 60-70°C, which is not compatible with the optimal growth temperature for Saccharomyces cerevisiae. In this study, 26 fungal strains producing amylolytic activities that were more active at 30°C than at 60°C were isolated from 151 environmental samples. Fungal strain WZ99, producing extracellular amylolytic activities with the lowest optimal temperature at 40°C, was identified as Aspergillus tritici by analysis of morphological and molecular data. An extracellular glucoamylase was purified from A. tritici WZ99. The optimal pH of the enzyme was 4.0-5.0 and optimal temperature was 45°C. The glucoamylase was stable at pH 4.5-10.0 and below 40°C. Metal ions at four concentrations did not inhibit the enzyme activity. The glucoamylase contained a catalytic domain belonging to glycosyl hydrolase family 15 and thus was named as AtriGA15A. The enzyme shared the highest identity of 54% with a glucoamylase from Rasamsonia emersonii. This glucoamylase showing excellent comprehensive enzymatic characteristics might have potential applications in starch-based bioethanol production and starch processing.
Collapse
Affiliation(s)
- Liang Xian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, China.
| |
Collapse
|
10
|
Trinh TMN, Holler M, Schneider JP, García-Moreno MI, García Fernández JM, Bodlenner A, Compain P, Ortiz Mellet C, Nierengarten JF. Construction of giant glycosidase inhibitors from iminosugar-substituted fullerene macromonomers. J Mater Chem B 2017; 5:6546-6556. [PMID: 32264416 DOI: 10.1039/c7tb01052d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An ultra-fast synthetic procedure based on grafting of twelve fullerene macromonomers onto a fullerene hexa-adduct core was used for the preparation of a giant molecule with 120 peripheral iminosugar residues. The inhibition profile of this giant iminosugar ball was evaluated against various glycosidases. In the particular case of the Jack bean α-mannosidase, a dramatic enhancement of the glycosidase inhibitory effect was observed for the giant molecule with 120 peripheral subunits as compared to that of the corresponding mono- and dodecavalent model compounds.
Collapse
Affiliation(s)
- Thi Minh Nguyet Trinh
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Miyazaki T, Nishikawa A, Tonozuka T. Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase. J Struct Biol 2016; 196:479-486. [PMID: 27688023 DOI: 10.1016/j.jsb.2016.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 01/28/2023]
Abstract
Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual 1S3 skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes.
Collapse
Affiliation(s)
- Takatsugu Miyazaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529 Japan; Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| |
Collapse
|
12
|
Schmidt AE, Shvetsov AV, Kuklin AI, Lebedev DV, Surzhik MA, Sergeev VR, Isaev-Ivanov VV. Small-angle scattering study of Aspergillus awamori glycoprotein glucoamylase. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516010223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Parasuram R, Mills CL, Wang Z, Somasundaram S, Beuning PJ, Ondrechen MJ. Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases. Methods 2016; 93:51-63. [DOI: 10.1016/j.ymeth.2015.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023] Open
|
14
|
Hua H, Luo H, Bai Y, Wang K, Niu C, Huang H, Shi P, Wang C, Yang P, Yao B. A thermostable glucoamylase from Bispora sp. MEY-1 with stability over a broad pH range and significant starch hydrolysis capacity. PLoS One 2014; 9:e113581. [PMID: 25415468 PMCID: PMC4240638 DOI: 10.1371/journal.pone.0113581] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 10/25/2014] [Indexed: 11/23/2022] Open
Abstract
Background Glucoamylase is an exo-type enzyme that converts starch completely into glucose from the non-reducing ends. To meet the industrial requirements for starch processing, a glucoamylase with excellent thermostability, raw-starch degradation ability and high glucose yield is much needed. In the present study we selected the excellent Carbohydrate-Activity Enzyme (CAZyme) producer, Bispora sp. MEY-1, as the microbial source for glucoamylase gene exploitation. Methodology/Principal Findings A glucoamylase gene (gla15) was cloned from Bispora sp. MEY-1 and successfully expressed in Pichia pastoris with a high yield of 34.1 U/ml. Deduced GLA15 exhibits the highest identity of 64.2% to the glucoamylase from Talaromyces (Rasamsonia) emersonii. Purified recombinant GLA15 was thermophilic and showed the maximum activity at 70°C. The enzyme was stable over a broad pH range (2.2–11.0) and at high temperature up to 70°C. It hydrolyzed the breakages of both α-1,4- and α-1,6-glycosidic linkages in amylopectin, soluble starch, amylose, and maltooligosaccharides, and had capacity to degrade raw starch. TLC and H1-NMR analysis showed that GLA15 is a typical glucoamylase of GH family 15 that releases glucose units from the non-reducing ends of α-glucans. The combination of Bacillus licheniformis amylase and GLA15 hydrolyzed 96.14% of gelatinized maize starch after 6 h incubation, which was about 9% higher than that of the combination with a commercial glucoamylase from Aspergillus niger. Conclusion/Significance GLA15 has a broad pH stability range, high-temperature thermostability, high starch hydrolysis capacity and high expression yield. In comparison with the commercial glucoamylase from A. niger, GLA15 represents a better candidate for application in the food industry including production of glucose, glucose syrups, and high-fructose corn syrups.
Collapse
Affiliation(s)
- Huifang Hua
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Kun Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Canfang Niu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Caihong Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- CAAS-ICRAF Joint Laboratory on Agroforestry and Sustainable Animal Husbandry, Beijing, 100193, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- * E-mail:
| |
Collapse
|
15
|
Ichikawa K, Tonozuka T, Uotsu-Tomita R, Akeboshi H, Nishikawa A, Sakano Y. Purification, Characterization, and Subsite Affinities ofThermoactinomyces vulgarisR-47 Maltooligosaccharide-metabolizing Enzyme Homologous to Glucoamylases. Biosci Biotechnol Biochem 2014; 68:413-20. [PMID: 14981306 DOI: 10.1271/bbb.68.413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A maltooligosaccharide-metabolizing enzyme from Thermoactinomyces vulgaris R-47 (TGA) homologous to glucoamylases does not degrade starch efficiently unlike most glucoamylases such as fungal glucoamylases (Uotsu-Tomita et al., Appl. Microbiol. Biotechnol., 56, 465-473 (2001)). In this study, we purified and characterized TGA, and determined the subsite affinities of the enzyme. The optimal pH and temperature of the enzyme are 6.8 and 60 degrees C, respectively. Activity assays with 0.4% substrate showed that TGA was most active against maltotriose, but did not prefer soluble starch. Kinetic analysis using maltooligosaccharides ranging from maltose to maltoheptaose revealed that TGA has high catalytic efficiency for maltotriose and maltose. Based on the kinetics, subsite affinities were determined. The A1+A2 value of this enzyme was highly positive whereas A4-A6 values were negative and little affinity was detected at subsites 3 and 7. Thus, the subsite structure of TGA is different from that of any other GA. The results indicate that TGA is a metabolizing enzyme specific for small maltooligosaccharides.
Collapse
Affiliation(s)
- Kazuhiro Ichikawa
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Japan
| | | | | | | | | | | |
Collapse
|
16
|
Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
Collapse
Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
| | | | | |
Collapse
|
17
|
Surzhik MA, Schmidt AE, Glazunov EA, Firsov DL, Petukhov MG. Introduction of additional thiol groups into glucoamylase in Aspergillus Awamori and their effect on the thermal stability and catalytic activity of the enzyme. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814020185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Miyazaki T, Ichikawa M, Yokoi G, Kitaoka M, Mori H, Kitano Y, Nishikawa A, Tonozuka T. Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. FEBS J 2013; 280:4560-71. [DOI: 10.1111/febs.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Takatsugu Miyazaki
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Megumi Ichikawa
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Gaku Yokoi
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Motomitsu Kitaoka
- National Food Research Institute; National Agriculture and Food Research Organization; Tsukuba Ibaraki Japan
| | - Haruhide Mori
- Research Faculty of Agriculture; Hokkaido University; Kita-ku Sapporo Japan
| | - Yoshikazu Kitano
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| |
Collapse
|
19
|
Sauer J, Abou Hachem M, Svensson B, Jensen KJ, Thygesen MB. Kinetic analysis of inhibition of glucoamylase and active site mutants via chemoselective oxime immobilization of acarbose on SPR chip surfaces. Carbohydr Res 2013; 375:21-8. [PMID: 23680647 DOI: 10.1016/j.carres.2013.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 10/26/2022]
Abstract
We here report a quantitative study on the binding kinetics of inhibition of the enzyme glucoamylase and how individual active site amino acid mutations influence kinetics. To address this challenge, we have developed a fast and efficient method for anchoring native acarbose to gold chip surfaces for surface plasmon resonance studies employing wild type glucoamylase and active site mutants, Y175F, E180Q, and R54L, as analytes. The key method was the chemoselective and protecting group-free oxime functionalization of the pseudo-tetrasaccharide-based inhibitor acarbose. By using this technique we have shown that at pH 7.0 the association and dissociation rate constants for the acarbose-glucoamylase interaction are 10(4)M(-1)s(-1) and 10(3)s(-1), respectively, and that the conformational change to a tight enzyme-inhibitor complex affects the dissociation rate constant by a factor of 10(2)s(-1). Additionally, the acarbose-presenting SPR surfaces could be used as a glucoamylase sensor that allowed rapid, label-free affinity screening of small carbohydrate-based inhibitors in solution, which is otherwise difficult with immobilized enzymes or other proteins.
Collapse
Affiliation(s)
- Jørgen Sauer
- Centre for Carbohydrate Recognition and Signalling, Department of Chemistry, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | | | | | | | | |
Collapse
|
20
|
Enzymatic Synthesis of Acarviosyl-maltooligosaccharides Using Disproportionating Enzyme 1. Biosci Biotechnol Biochem 2013; 77:312-9. [DOI: 10.1271/bbb.120732] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
21
|
Forcella M, Mozzi A, Bigi A, Parenti P, Fusi P. Molecular cloning of soluble trehalase from Chironomus riparius larvae, its heterologous expression in Escherichia coli and bioinformatic analysis. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2012; 81:77-89. [PMID: 22851493 DOI: 10.1002/arch.21041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Trehalase is involved in the control of trehalose concentration, the main blood sugar in insects. Here, we describe the molecular cloning of the cDNA encoding for the soluble form of the trehalase from the midge larvae of Chironomus riparius, a well-known bioindicator of the quality of freshwater environments. Molecular cloning was achieved through multiple alignment of Diptera trehalase sequences, allowing the synthesis of internal homology-based primers; the complete open reading frame(ORF) was subsequently obtained through RACE-PCR(where RACE is rapid amplification of cDNA ends). The cDNA contained the 5' untranslated region (UTR), the 3' UTR including a poly(A) tail and the ORF of 1,725 bp consisting of 574 amino acid residues with a predicted molecular mass of 65,778 Da. Recombinant trehalase was successfully expressed in Escherichia coli as a His-tagged protein and purified on Ni-NTA affinity chromatography. Primary structure analysis showed a series of characteristic features shared by all insect trehalases, while three-dimensional structure prediction yielded the typical glucosidase fold, the two key residues involved in the catalytic mechanism being conserved. Production of recombinant insect trehalases opens the way to structural characterizations of the catalytic site, which might represent, among others, an element for reconsidering the enzyme as a target in pest insects' control.
Collapse
Affiliation(s)
- Matilde Forcella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
| | | | | | | | | |
Collapse
|
22
|
Andrioli WJ, Silva TM, da Silva VB, Damásio AR, Maller A, Conti R, Jorge JA, Araújo JM, Silva CH, Pupo MT, Polizeli ML, Bastos JK. The fungal metabolite eugenitin as additive for Aspergillus niveus glucoamylase activation. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
23
|
Putative stress sensors WscA and WscB are involved in hypo-osmotic and acidic pH stress tolerance in Aspergillus nidulans. EUKARYOTIC CELL 2011; 10:1504-15. [PMID: 21926329 DOI: 10.1128/ec.05080-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Wsc proteins have been identified in fungi and are believed to be stress sensors in the cell wall integrity (CWI) signaling pathway. In this study, we characterized the sensor orthologs WscA and WscB in Aspergillus nidulans. Using hemagglutinin-tagged WscA and WscB, we showed both Wsc proteins to be N- and O-glycosylated and localized in the cell wall and membrane, implying that they are potential cell surface sensors. The wscA disruptant (ΔwscA) strain was characterized by reduced colony and conidia formation and a high frequency of swollen hyphae under hypo-osmotic conditions. The deficient phenotype of the ΔwscA strain was facilitated by acidification, but not by alkalization or antifungal agents. In contrast, osmotic stabilization restored the normal phenotype in the ΔwscA strain. A similar inhibition was observed in the wscB disruptant strain, but to a lesser extent. In addition, a double wscA and wscB disruptant (ΔwscA ΔwscB) strain was viable, but its growth was inhibited to a greater degree, indicating that the functions of the products of these genes are redundant. Transcription of α-1,3-glucan synthase genes (agsA and agsB) was significantly altered in the wscA disruptant strain, resulting in an increase in the amount of alkali-soluble cell wall glucan compared to that in the wild-type (wt) strain. An increase in mitogen-activated protein kinase (MpkA) phosphorylation was observed as a result of wsc disruption. Moreover, the transient transcriptional upregulation of the agsB gene via MpkA signaling was observed in the ΔwscA ΔwscB strain to the same degree as in the wt strain. These results indicate that A. nidulans Wsc proteins have a different sensing spectrum and downstream signaling pathway than those in the yeast Saccharomyces cerevisiae and that they play an important role in CWI under hypo-osmotic and acidic pH conditions.
Collapse
|
24
|
Schlamadinger DE, Daschbach MM, Gokel GW, Kim JE. UV resonance Raman study of cation-π interactions in an indole crown ether. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2011; 42:633-638. [PMID: 25635155 PMCID: PMC4307609 DOI: 10.1002/jrs.2781] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
UV resonance Raman (UVRR) spectroscopy is used to probe changes in vibrational structure associated with cation-π interactions for the most prevalent amino acid π -donor, tryptophan. The model compound studied here is a diaza crown ether with two indole substituents. In the presence of sodium or potassium sequestered in the crown ether, or a protonated diaza group on the compound, the indole moieties participate in a cation-π interaction in which the pyrrolo group acts as the primary π-donor. Systematic shifts in relative intensity in the 760-780 cm-1 region are observed upon formation of this cation-π interaction; we propose that these modifications reflect shifts of the delocalized, ring-breathing W18 and hydrogen-out-of-plane (HOOP) vibrational modes in this spectral region. The observed changes are attributed to perturbations of the π-electron density as well as of normal modes that involve large displacement of the hydrogen atom on the C2 position of the pyrrole ring. Modest variations in the UVRR spectra for the three complexes studied here are correlated to differences in cation-π strength. Specifically, the UVRR spectrum of the sodium-bound complex differs from those of the potassium-bound or protonated-diaza complexes, and may reflect the observation that the C2 hydrogen atom in the sodium-bound complex exhibits the greatest perturbation relative to the other species. Normal modes sensitive to hydrogen-bonding, such as the tryptophan W10, W9, and W8 modes, also undergo shifts in the presence of the salts. These shifts reflect the strength of interaction of the indole N-H group with the iodide or hexafluorophosphate counteranion. The current observation that the W18 and HOOP normal mode regions of the indole crown ether compound are sensitive to cation-pyrrolo π interactions suggests that this region may provide reliable spectroscopic evidence of these important interactions in proteins.
Collapse
Affiliation(s)
- Diana E. Schlamadinger
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 USA
| | | | - George W. Gokel
- Department of Chemistry, Washington University, St. Louis, MO 63110 USA
- Departments of Chemistry and Biochemistry, and Biology, Center for Nanoscience, University of Missouri – St. Louis, St. Louis, MO 63121 USA
- Department of Developmental Biology, Washington University, St. Louis, MO 63110 USA
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 USA
- Correspondence to: Judy E. Kim, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA.
| |
Collapse
|
25
|
Bonaccini C, Chioccioli M, Parmeggiani C, Cardona F, Lo Re D, Soldaini G, Vogel P, Bello C, Goti A, Gratteri P. Synthesis, Biological Evaluation and Docking Studies of Casuarine Analogues: Effects of Structural Modifications at Ring B on Inhibitory Activity Towards Glucoamylase. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000632] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
26
|
Nakai H, Hachem MA, Petersen BO, Westphal Y, Mannerstedt K, Baumann MJ, Dilokpimol A, Schols HA, Duus JØ, Svensson B. Efficient chemoenzymatic oligosaccharide synthesis by reverse phosphorolysis using cellobiose phosphorylase and cellodextrin phosphorylase from Clostridium thermocellum. Biochimie 2010; 92:1818-26. [PMID: 20678539 DOI: 10.1016/j.biochi.2010.07.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 07/22/2010] [Indexed: 11/30/2022]
Abstract
Inverting cellobiose phosphorylase (CtCBP) and cellodextrin phosphorylase (CtCDP) from Clostridium thermocellum ATCC27405 of glycoside hydrolase family 94 catalysed reverse phosphorolysis to produce cellobiose and cellodextrins in 57% and 48% yield from α-d-glucose 1-phosphate as donor with glucose and cellobiose as acceptor, respectively. Use of α-d-glucosyl 1-fluoride as donor increased product yields to 98% for CtCBP and 68% for CtCDP. CtCBP showed broad acceptor specificity forming β-glucosyl disaccharides with β-(1→4)- regioselectivity from five monosaccharides as well as branched β-glucosyl trisaccharides with β-(1→4)-regioselectivity from three (1→6)-linked disaccharides. CtCDP showed strict β-(1→4)-regioselectivity and catalysed linear chain extension of the three β-linked glucosyl disaccharides, cellobiose, sophorose, and laminaribiose, whereas 12 tested monosaccharides were not acceptors. Structure analysis by NMR and ESI-MS confirmed two β-glucosyl oligosaccharide product series to represent novel compounds, i.e. β-D-glucopyranosyl-[(1→4)-β-D-glucopyranosyl](n)-(1→2)-D-glucopyranose, and β-D-glucopyranosyl-[(1→4)-β-D-glucopyranosyl](n)-(1→3)-D-glucopyranose (n = 1-7). Multiple sequence alignment together with a modelled CtCBP structure, obtained using the crystal structure of Cellvibrio gilvus CBP in complex with glucose as a template, indicated differences in the subsite +1 region that elicit the distinct acceptor specificities of CtCBP and CtCDP. Thus Glu636 of CtCBP recognized the C1 hydroxyl of β-glucose at subsite +1, while in CtCDP the presence of Ala800 conferred more space, which allowed accommodation of C1 substituted disaccharide acceptors at the corresponding subsites +1 and +2. Furthermore, CtCBP has a short Glu496-Thr500 loop that permitted the C6 hydroxyl of glucose at subsite +1 to be exposed to solvent, whereas the corresponding longer loop Thr637-Lys648 in CtCDP blocks binding of C6-linked disaccharides as acceptors at subsite +1. High yields in chemoenzymatic synthesis, a novel regioselectivity, and novel oligosaccharides including products of CtCDP catalysed oligosaccharide oligomerisation using α-d-glucosyl 1-fluoride, all together contribute to the formation of an excellent basis for rational engineering of CBP and CDP to produce desired oligosaccharides.
Collapse
Affiliation(s)
- Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Catalytic Properties of Two Rhizopus oryzae 99-880 Glucoamylase Enzymes Without Starch Binding Domains Expressed in Pichia pastoris. Appl Biochem Biotechnol 2010; 162:2197-213. [DOI: 10.1007/s12010-010-8994-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/26/2022]
|
28
|
Kumar A, Alam MA, Rani S, Vankar YD. Synthesis of 1,4-dideoxy-1,4-iminoheptitol and 1,5-dideoxy-1,5-iminooctitols from d-xylose. Carbohydr Res 2010; 345:1142-8. [DOI: 10.1016/j.carres.2010.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/05/2010] [Accepted: 04/18/2010] [Indexed: 10/19/2022]
|
29
|
Surzhik MA, Churkina SV, Shmidt AE, Shvetsov AV, Kozhina TN, Firsov DL, Firsov LM, Petukhov MG. The effect of point amino acid substitutions in an internal α-helix on thermostability of Aspergillus awamori X100 glucoamylase. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810020134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
30
|
Kumar P, Satyanarayana T. Microbial glucoamylases: characteristics and applications. Crit Rev Biotechnol 2009; 29:225-55. [DOI: 10.1080/07388550903136076] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
31
|
Characterization of a Neutral and Thermostable Glucoamylase from the Thermophilic Mold Thermomucor indicae-seudaticae: Activity, Stability, and Structural Correlation. Appl Biochem Biotechnol 2009; 160:879-90. [DOI: 10.1007/s12010-009-8666-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 05/04/2009] [Indexed: 11/26/2022]
|
32
|
Thygesen M, Sauer J, Jensen K. Chemoselective Capture of Glycans for Analysis on Gold Nanoparticles: Carbohydrate Oxime Tautomers Provide Functional Recognition by Proteins. Chemistry 2009; 15:1649-60. [DOI: 10.1002/chem.200801521] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
Cheng J, Luo X, Yan X, Li Z, Tang Y, Jiang H, Zhu W. Research progress in cation-π interactions. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11426-008-0082-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
34
|
Hill AD, Reilly PJ. A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem 2008; 29:1131-41. [PMID: 18074341 DOI: 10.1002/jcc.20873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.
Collapse
Affiliation(s)
- Anthony D Hill
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
| | | |
Collapse
|
35
|
Bott R, Saldajeno M, Cuevas W, Ward D, Scheffers M, Aehle W, Karkehabadi S, Sandgren M, Hansson H. Three-dimensional structure of an intact glycoside hydrolase family 15 glucoamylase from Hypocrea jecorina. Biochemistry 2008; 47:5746-54. [PMID: 18457422 DOI: 10.1021/bi702413k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The three-dimensional structure of a complete Hypocrea jecorina glucoamylase has been determined at 1.8 A resolution. The presented structure model includes the catalytic and starch binding domains and traces the course of the 37-residue linker segment. While the structures of other fungal and yeast glucoamylase catalytic and starch binding domains have been determined separately, this is the first intact structure that allows visualization of the juxtaposition of the starch binding domain relative to the catalytic domain. The detailed interactions we see between the catalytic and starch binding domains are confirmed in a second independent structure determination of the enzyme in a second crystal form. This second structure model exhibits an identical conformation compared to the first structure model, which suggests that the H. jecorina glucoamylase structure we report is independent of crystal lattice contact restraints and represents the three-dimensional structure found in solution. The proposed starch binding regions for the starch binding domain are aligned with the catalytic domain in the three-dimensional structure in a manner that supports the hypothesis that the starch binding domain serves to target the glucoamylase at sites where the starch granular matrix is disrupted and where the enzyme might most effectively function.
Collapse
Affiliation(s)
- Richard Bott
- Genencor-A Danisco Division, 925 Page Mill Road, Palo Alto, California 94304, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
|
37
|
Abstract
The production by filamentous fungi of therapeutic glycoproteins intended for use in mammals is held back by the inherent difference in protein N-glycosylation and by the inability of the fungal cell to modify proteins with mammalian glycosylation structures. Here, we report protein N-glycan engineering in two Aspergillus species. We functionally expressed in the fungal hosts heterologous chimeric fusion proteins containing different localization peptides and catalytic domains. This strategy allowed the isolation of a strain with a functional alpha-1,2-mannosidase producing increased amounts of N-glycans of the Man5GlcNAc2 type. This strain was further engineered by the introduction of a functional GlcNAc transferase I construct yielding GlcNAcMan5GlcNac2 N-glycans. Additionally, we deleted algC genes coding for an enzyme involved in an early step of the fungal glycosylation pathway yielding Man3GlcNAc2 N-glycans. This modification of fungal glycosylation is a step toward the ability to produce humanized complex N-glycans on therapeutic proteins in filamentous fungi.
Collapse
|
38
|
Sterner B, Singh R, Berger B. Predicting and annotating catalytic residues: an information theoretic approach. J Comput Biol 2007; 14:1058-73. [PMID: 17887954 DOI: 10.1089/cmb.2007.0042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We introduce a computational method to predict and annotate the catalytic residues of a protein using only its sequence information, so that we describe both the residues' sequence locations (prediction) and their specific biochemical roles in the catalyzed reaction (annotation). While knowing the chemistry of an enzyme's catalytic residues is essential to understanding its function, the challenges of prediction and annotation have remained difficult, especially when only the enzyme's sequence and no homologous structures are available. Our sequence-based approach follows the guiding principle that catalytic residues performing the same biochemical function should have similar chemical environments; it detects specific conservation patterns near in sequence to known catalytic residues and accordingly constrains what combination of amino acids can be present near a predicted catalytic residue. We associate with each catalytic residue a short sequence profile and define a Kullback-Leibler (KL) distance measure between these profiles, which, as we show, effectively captures even subtle biochemical variations. We apply the method to the class of glycohydrolase enzymes. This class includes proteins from 96 families with very different sequences and folds, many of which perform important functions. In a cross-validation test, our approach correctly predicts the location of the enzymes' catalytic residues with a sensitivity of 80% at a specificity of 99.4%, and in a separate cross-validation we also correctly annotate the biochemical role of 80% of the catalytic residues. Our results compare favorably to existing methods. Moreover, our method is more broadly applicable because it relies on sequence and not structure information; it may, furthermore, be used in conjunction with structure-based methods.
Collapse
Affiliation(s)
- Beckett Sterner
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | |
Collapse
|
39
|
Michelin M, Ruller R, Ward RJ, Moraes LAB, Jorge JA, Terenzi HF, Polizeli MDLTM. Purification and biochemical characterization of a thermostable extracellular glucoamylase produced by the thermotolerant fungus Paecilomyces variotii. J Ind Microbiol Biotechnol 2007; 35:17-25. [DOI: 10.1007/s10295-007-0261-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 09/18/2007] [Indexed: 11/29/2022]
|
40
|
Gibson RP, Gloster TM, Roberts S, Warren RAJ, Storch de Gracia I, García A, Chiara JL, Davies GJ. Molecular Basis for Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors. Angew Chem Int Ed Engl 2007; 46:4115-9. [PMID: 17455176 DOI: 10.1002/anie.200604825] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert P Gibson
- Department of Chemistry, York Structural Biology Laboratory, York, YO, UK
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Gibson R, Gloster T, Roberts S, Warren R, Storch de Gracia I, García Á, Chiara J, Davies G. Molecular Basis for Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
42
|
Cheng J, Gong Z, Zhu W, Tang Y, Li W, Li Z, Jiang H. Cation sitting in aromatic cages:ab initio computational studies on tetramethylammonium–(benzene)n (n=3–4) complexes. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1175] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
43
|
Sevcík J, Hostinová E, Solovicová A, Gasperík J, Dauter Z, Wilson KS. Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain. FEBS J 2006; 273:2161-71. [PMID: 16649993 DOI: 10.1111/j.1742-4658.2006.05230.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most glucoamylases (alpha-1,4-D-glucan glucohydrolase, EC 3.2.1.3) have structures consisting of both a catalytic and a starch binding domain. The structure of a glucoamylase from Saccharomycopsis fibuligera HUT 7212 (Glu), determined a few years ago, consists of a single catalytic domain. The structure of this enzyme with the resolution extended to 1.1 A and that of the enzyme-acarbose complex at 1.6 A resolution are presented here. The structure at atomic resolution, besides its high accuracy, shows clearly the influence of cryo-cooling, which is manifested in shrinkage of the molecule and lowering the volume of the unit cell. In the structure of the complex, two acarbose molecules are bound, one at the active site and the second at a site remote from the active site, curved around Tyr464 which resembles the inhibitor molecule in the 'sugar tongs' surface binding site in the structure of barley alpha-amylase isozyme 1 complexed with a thiomalto-oligosaccharide. Based on the close similarity in sequence of glucoamylase Glu, which does not degrade raw starch, to that of glucoamylase (Glm) from S. fibuligera IFO 0111, a raw starch-degrading enzyme, it is reasonable to expect the presence of the remote starch binding site at structurally equivalent positions in both enzymes. We propose the role of this site is to fix the enzyme onto the surface of a starch granule while the active site degrades the polysaccharide. This hypothesis is verified here by the preparation of mutants of glucoamylases Glu and Glm.
Collapse
Affiliation(s)
- Jozef Sevcík
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia.
| | | | | | | | | | | |
Collapse
|
44
|
Abstract
We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes. Furthermore, carbohydrate-modifying proteins such as glycosyl hydrolases and phosphorylases are of growing importance as potential drug targets. Interactions between proteins and carbohydrates have complex thermodynamics, and in general the specific positioning of only a few hydroxyl groups determines their binding affinities. A thorough understanding of both carbohydrate and protein structures is thus essential to predict these interactions. An atomic-level view of carbohydrate recognition through structures of carbohydrate-active enzymes complexed with transition-state inhibitors reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. However, the inherent flexibility of carbohydrates and their often water-mediated hydrogen bonding to proteins makes simulation of their complexes difficult. Nonetheless, recent developments such as the parameterization of specific force fields and docking scoring functions have greatly improved our ability to predict protein-carbohydrate interactions. We review protein-carbohydrate complexes having defined molecular requirements for specific carbohydrate recognition by proteins, providing an overview of the different computational techniques available to model them.
Collapse
Affiliation(s)
- Alain Laederach
- Department of Chemical Engineering, Iowa State University, Ames, Iowa 50011-2230, USA
| | | |
Collapse
|
45
|
Morimoto N, Yasukawa Y, Watanabe K, Unno T, Ito H, Matsui H. Cloning and heterologous expression of a glucodextranase gene from Arthrobacter globiformis I42, and experimental evidence for the catalytic diad of the recombinant enzyme. J Biosci Bioeng 2005; 97:127-30. [PMID: 16233603 DOI: 10.1016/s1389-1723(04)70179-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Accepted: 10/31/2003] [Indexed: 11/18/2022]
Abstract
The gene encoding a glucodextranase from Arthrobacter globiformis I42 was cloned and, subsequently, heterologously expressed in Escherichia coli. This glucodextranase gene consists of 1048 amino acid residues with a calculated molecular mass of 109,135 Da. The roles of two residues at the active site of A. globiformis I42 glucodextranase were examined by site-directed mutagenesis. Glutamic acid residues 458 and 656, which are part of the apparent catalytic residues, were found to be essential for hydrolase activity.
Collapse
Affiliation(s)
- Naoki Morimoto
- Department of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Sapporo 060-8589, Japan
| | | | | | | | | | | |
Collapse
|
46
|
Ichikawa K, Tonozuka T, Mizuno M, Nishikawa A, Sakano Y. Site-Directed Mutagenesis of Tryptophan 622 of Thermoactinomyces vulgaris R-47 Glucoamylase: pH Optima and Activities of Five Mutants. J Appl Glycosci (1999) 2005. [DOI: 10.5458/jag.52.277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
47
|
Mizuno M, Tonozuka T, Ichikawa K, Kamitori S, Nishikawa A, Sakano Y. X-ray Crystallographic Study of Glucodextranase from a Gram-positive Bacterium, Arthrobacter globiformis I42. J Appl Glycosci (1999) 2005. [DOI: 10.5458/jag.52.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
48
|
Liu T, Zhu W, Gu J, Shen J, Luo X, Chen G, Puah CM, Silman I, Chen K, Sussman JL, Jiang H. Additivity of Cation−π Interactions: An ab Initio Computational Study on π−Cation−π Sandwich Complexes. J Phys Chem A 2004. [DOI: 10.1021/jp0476850] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tong Liu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Weiliang Zhu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jiandu Gu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jianhua Shen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiaomin Luo
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gang Chen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Chum Mok Puah
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Israel Silman
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Kaixian Chen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Joel L. Sussman
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hualiang Jiang
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| |
Collapse
|
49
|
Kimura A, Lee JH, Lee IS, Lee HS, Park KH, Chiba S, Kim D. Two potent competitive inhibitors discriminating α-glucosidase family I from family II. Carbohydr Res 2004; 339:1035-40. [PMID: 15063189 DOI: 10.1016/j.carres.2003.10.035] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Accepted: 12/28/2003] [Indexed: 11/23/2022]
Abstract
The inhibition kinetics for isoacarbose (a pseudotetrasaccharide, IsoAca) and acarviosine-glucose (pseudotrisaccharide, AcvGlc), both of which are derivatives of acarbose, were investigated with various types of alpha-glucosidases obtained from microorganisms, plants, and insects. IsoAca and AcvGlc, competitive inhibitors, allowed classification of alpha-glucosidases into two groups. Enzymes of the first group were strongly inhibited by AcvGlc and weakly by IsoAca, in which the K(i) values of AcvGlc (0.35-3.0 microM) were 21- to 440-fold smaller than those of IsoAca. However, the second group of enzymes showed similar K(i) values, ranging from 1.6 to 8.0 microM for both compounds. This classification for alpha-glucosidases is in total agreement with that based on the similarity of their amino acid sequences (family I and family II). This indicated that the alpha-glucosidase families I and II could be clearly distinguished based on their inhibition kinetic data for IsoAca and AcvGlc. The two groups of alpha-glucosidases seemed to recognize distinctively the extra reducing-terminal glucose unit in IsoAca.
Collapse
Affiliation(s)
- Atsuo Kimura
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
| | | | | | | | | | | | | |
Collapse
|
50
|
Mizuno M, Tonozuka T, Suzuki S, Uotsu-Tomita R, Kamitori S, Nishikawa A, Sakano Y. Structural insights into substrate specificity and function of glucodextranase. J Biol Chem 2003; 279:10575-83. [PMID: 14660574 DOI: 10.1074/jbc.m310771200] [Citation(s) in RCA: 40] [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
A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end to produce beta-D-glucose via an inverting reaction mechanism and classified into the glycoside hydrolase family 15 (GH15). Here we cloned the iGDase gene and determined the crystal structures of iGDase of the unliganded form and the complex with acarbose at 2.42-A resolution. The structure of iGDase is composed of four domains N, A, B, and C. Domain A forms an (alpha/alpha)(6)-barrel structure and domain N consists of 17 antiparallel beta-strands, and both domains are conserved in bacterial glucoamylases (GAs) and appear to be mainly concerned with catalytic activity. The structure of iGDase complexed with acarbose revealed that the positions and orientations of the residues at subsites -1 and +1 are nearly identical between iGDase and GA; however, the residues corresponding to subsite 3, which form the entrance of the substrate binding pocket, and the position of the open space and constriction of iGDase are different from those of GAs. On the other hand, domains B and C are not found in the bacterial GAs. The primary structure of domain C is homologous with a surface layer homology domain of pullulanases, and the three-dimensional structure of domain C resembles the carbohydrate-binding domain of some glycohydrolases.
Collapse
Affiliation(s)
- Masahiro Mizuno
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | | | | | | | | | | | | |
Collapse
|