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Wangpaiboon K, Laohawuttichai P, Kim SY, Mori T, Nakapong S, Pichyangkura R, Pongsawasdi P, Hakoshima T, Krusong K. A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1064-1076. [PMID: 34342279 DOI: 10.1107/s205979832100677x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
α-Glucosidase (EC 3.2.1.20) is a carbohydrate-hydrolyzing enzyme which generally cleaves α-1,4-glycosidic bonds of oligosaccharides and starch from the nonreducing ends. In this study, the novel α-glucosidase from Weissella cibaria BBK-1 (WcAG) was biochemically and structurally characterized. WcAG belongs to glycoside hydrolase family 13 (GH13) and to the neopullanase subfamily. It exhibits distinct hydrolytic activity towards the α-1,4 linkages of short-chain oligosaccharides from the reducing end. The enzyme prefers to hydrolyse maltotriose and acarbose, while it cannot hydrolyse cyclic oligosaccharides and polysaccharides. In addition, WcAG can cleave pullulan hydrolysates and strongly exhibits transglycosylation activity in the presence of maltose. Size-exclusion chromatography and X-ray crystal structures revealed that WcAG forms a homodimer in which the N-terminal domain of one monomer is orientated in proximity to the catalytic domain of another, creating the substrate-binding groove. Crystal structures of WcAG in complexes with maltose, maltotriose and acarbose revealed a remarkable enzyme active site with accessible +2, +1 and -1 subsites, along with an Arg-Glu gate (Arg176-Glu296) in front of the active site. The -2 and -3 subsites were blocked by Met119 and Asn120 from the N-terminal domain of a different subunit, resulting in an extremely restricted substrate preference.
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Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pasunee Laohawuttichai
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sun Yong Kim
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Mori
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Santhana Nakapong
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piamsook Pongsawasdi
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Toshio Hakoshima
- Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara 630-0192, Japan
| | - Kuakarun Krusong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis. J Biol Chem 2018; 293:16874-16888. [PMID: 30181215 PMCID: PMC6204909 DOI: 10.1074/jbc.ra118.004472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Indexed: 01/07/2023] Open
Abstract
Cyclic α-maltosyl-(1→6)-maltose (CMM, cyclo-{→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→6)-α-d-Glcp-(1→4)-α-d-Glcp-(1→})is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. CMM is composed of two maltose units and is one of the smallest cyclic glucooligosaccharides. Although CMM is resistant to usual amylases, it is efficiently hydrolyzed by CMM hydrolase (CMMase), belonging to subfamily 20 of glycoside hydrolase family 13 (GH13_20). Here, we determined the ligand-free crystal structure of CMMase from the soil-associated bacterium Arthrobacter globiformis and its structures in complex with maltose, panose, and CMM to elucidate the structural basis of substrate recognition by CMMase. The structures disclosed that although the monomer structure consists of three domains commonly adopted by GH13 and other α-amylase-related enzymes, CMMase forms a unique wing-like dimer structure. The complex structure with CMM revealed four specific subsites, namely -3', -2, -1, and +1'. We also observed that the bound CMM molecule adopts a low-energy conformer compared with the X-ray structure of a single CMM crystal, also determined here. Comparison of the CMMase active site with those in other enzymes of the GH13_20 family revealed that three regions forming the wall of the cleft, denoted PYF (Pro-203/Tyr-204/Phe-205), CS (Cys-163/Ser-164), and Y (Tyr-168), are present only in CMMase and are involved in CMM recognition. Combinations of multiple substitutions in these regions markedly decreased the activity toward CMM, indicating that the specificity for this cyclic tetrasaccharide is supported by the entire shape of the pocket. In summary, our work uncovers the mechanistic basis for the highly specific interactions of CMMase with its substrate CMM.
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Guo J, Coker AR, Wood SP, Cooper JB, Keegan RM, Ahmad N, Muhammad MA, Rashid N, Akhtar M. Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:305-314. [PMID: 29652257 DOI: 10.1107/s2059798318001754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/29/2018] [Indexed: 11/10/2022]
Abstract
Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100°C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Alun R Coker
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Steve P Wood
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Jonathan B Cooper
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Ronan M Keegan
- CCP4, Research Complex at Harwell and Science and Technology Facilities Council, Rutherford Appleton Laboratories, Harwell Oxford, Didcot OX11 0FA, England
| | - Nasir Ahmad
- Institute of Agricultural Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Majida Atta Muhammad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhummad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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4
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Kuchtová A, Janeček Š. Domain evolution in enzymes of the neopullulanase subfamily. Microbiology (Reading) 2016; 162:2099-2115. [DOI: 10.1099/mic.0.000390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea Kuchtová
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Štefan Janeček
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
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Møller MS, Henriksen A, Svensson B. Structure and function of α-glucan debranching enzymes. Cell Mol Life Sci 2016; 73:2619-41. [PMID: 27137180 PMCID: PMC11108273 DOI: 10.1007/s00018-016-2241-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
Abstract
α-Glucan debranching enzymes hydrolyse α-1,6-linkages in starch/glycogen, thereby, playing a central role in energy metabolism in all living organisms. They belong to glycoside hydrolase families GH13 and GH57 and several of these enzymes are industrially important. Nine GH13 subfamilies include α-glucan debranching enzymes; isoamylase and glycogen debranching enzymes (GH13_11); pullulanase type I/limit dextrinase (GH13_12-14); pullulan hydrolase (GH13_20); bifunctional glycogen debranching enzyme (GH13_25); oligo-1 and glucan-1,6-α-glucosidases (GH13_31); pullulanase type II (GH13_39); and α-amylase domains (GH13_41) in two-domain amylase-pullulanases. GH57 harbours type II pullulanases. Specificity differences, domain organisation, carbohydrate binding modules, sequence motifs, three-dimensional structures and specificity determinants are discussed. The phylogenetic analysis indicated that GH13_39 enzymes could represent a "missing link" between the strictly α-1,6-specific debranching enzymes and the enzymes with dual specificity and α-1,4-linkage preference.
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Affiliation(s)
- Marie Sofie Møller
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00, Lund, Sweden.
| | - Anette Henriksen
- Global Research Unit, Department of Large Protein Biophysics and Formulation, Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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6
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Manas NHA, Bakar FDA, Illias RM. Computational docking, molecular dynamics simulation and subsite structure analysis of a maltogenic amylase from Bacillus lehensis G1 provide insights into substrate and product specificity. J Mol Graph Model 2016; 67:1-13. [DOI: 10.1016/j.jmgm.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/14/2016] [Accepted: 04/18/2016] [Indexed: 10/21/2022]
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7
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Ahmad N, Mehboob S, Rashid N. Starch-processing enzymes — emphasis on thermostable 4-α-glucanotransferases. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Abdul Manas NH, Jonet MA, Abdul Murad AM, Mahadi NM, Illias RM. Modulation of transglycosylation and improved malto-oligosaccharide synthesis by protein engineering of maltogenic amylase from Bacillus lehensis G1. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Koo YS, Lee HW, Jeon HY, Choi HJ, Choung WJ, Shim JH. Development and characterization of cyclodextrin glucanotransferase as a maltoheptaose-producing enzyme using site-directed mutagenesis. Protein Eng Des Sel 2015; 28:531-7. [DOI: 10.1093/protein/gzv044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/09/2015] [Indexed: 11/14/2022] Open
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10
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Kobayashi M, Saburi W, Nakatsuka D, Hondoh H, Kato K, Okuyama M, Mori H, Kimura A, Yao M. Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase. FEBS Lett 2015; 589:484-9. [PMID: 25595454 DOI: 10.1016/j.febslet.2015.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/05/2015] [Accepted: 01/05/2015] [Indexed: 11/16/2022]
Abstract
Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form α-(1→6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4Å resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG.
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Affiliation(s)
- Momoko Kobayashi
- Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Daichi Nakatsuka
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Hironori Hondoh
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan
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11
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Tamamura N, Saburi W, Mukai A, Morimoto N, Takehana T, Koike S, Matsui H, Mori H. Enhancement of hydrolytic activity of thermophilic alkalophilic α-amylase from Bacillus sp. AAH-31 through optimization of amino acid residues surrounding the substrate binding site. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Ben Mabrouk S, Ayadi-Zouari D, Ben Hlima H, Bejar S. Changes in the catalytic properties and substrate specificity of Bacillus sp. US149 maltogenic amylase by mutagenesis of residue 46. ACTA ACUST UNITED AC 2013; 40:947-53. [DOI: 10.1007/s10295-013-1300-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/29/2013] [Indexed: 11/30/2022]
Abstract
Abstract
Maltogenic amylase from Bacillus sp. US149 (MAUS149) is a cyclodextrin (CD)-degrading enzyme with a high preference for CDs over maltooligosaccharides. In this study, we investigated the roles of residue Asp46 in the specificity and catalytic properties of MAUS149 by using site-directed mutagenesis. Three mutated enzymes (D46V, D46G and D46N) were constructed and studied. The three mutants were found to be similar to the wild-type MAUS149 regarding thermoactivity, thermostability and pH profile. Nevertheless, the kinetic parameters for all the substrates of the mutant enzymes D46V and D46G were altered enormously as compared with those of the wild type. Indeed, the K m values of MAUS149/D46G for all substrates were strongly increased. Nevertheless, the affinity and catalytic efficiency of MAUS149/D46V toward β-CD were increased fivefold as compared with those of MAUS149. Molecular modelling suggests that residue D46 forms a salt bridge with residue K282. This bond would maintain the arrangement of side chains of residues Y45 and W47 in a particular orientation that promotes access to the catalytic site and maintains the substrate therein. Hence, any replacement with uncharged amino acids influenced the flexibility of the gate wall at the substrate binding cleft resulting in changes in substrate selectivity.
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Affiliation(s)
- Sameh Ben Mabrouk
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Dorra Ayadi-Zouari
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Hajer Ben Hlima
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
| | - Samir Bejar
- grid.412124.0 0000000123235644 Laboratoire de Métabolites Et de Biomolécules, Centre de Biotechnologie de Sfax Université de Sfax BP 1177 3018 Sfax Tunisia
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Nishiyama M, Yamamoto S, Kurosawa N. Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches. J Microbiol 2013; 51:413-22. [PMID: 23990291 DOI: 10.1007/s12275-013-2419-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/07/2013] [Indexed: 11/29/2022]
Abstract
Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.
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Affiliation(s)
- Minako Nishiyama
- Department of Environmental Engineering for Symbiosis, Faculty of Engineering, Soka University, Tokyo 192-8577, Japan
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Jung TY, Li D, Park JT, Yoon SM, Tran PL, Oh BH, Janeček Š, Park SG, Woo EJ, Park KH. Association of novel domain in active site of archaic hyperthermophilic maltogenic amylase from Staphylothermus marinus. J Biol Chem 2012; 287:7979-89. [PMID: 22223643 DOI: 10.1074/jbc.m111.304774] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylothermus marinus maltogenic amylase (SMMA) is a novel extreme thermophile maltogenic amylase with an optimal temperature of 100 °C, which hydrolyzes α-(1-4)-glycosyl linkages in cyclodextrins and in linear malto-oligosaccharides. This enzyme has a long N-terminal extension that is conserved among archaic hyperthermophilic amylases but is not found in other hydrolyzing enzymes from the glycoside hydrolase 13 family. The SMMA crystal structure revealed that the N-terminal extension forms an N' domain that is similar to carbohydrate-binding module 48, with the strand-loop-strand region forming a part of the substrate binding pocket with several aromatic residues, including Phe-95, Phe-96, and Tyr-99. A structural comparison with conventional cyclodextrin-hydrolyzing enzymes revealed a striking resemblance between the SMMA N' domain position and the dimeric N domain position in bacterial enzymes. This result suggests that extremophilic archaea that live at high temperatures may have adopted a novel domain arrangement that combines all of the substrate binding components within a monomeric subunit. The SMMA structure provides a molecular basis for the functional properties that are unique to hyperthermophile maltogenic amylases from archaea and that distinguish SMMA from moderate thermophilic or mesophilic bacterial enzymes.
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Affiliation(s)
- Tae-Yang Jung
- Department of Biological Sciences, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-701, Korea
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15
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Enzymatic synthesis of novel branched sugar alcohols mediated by the transglycosylation reaction of pullulan-hydrolyzing amylase II (TVA II) cloned from Thermoactinomyces vulgaris R-47. Carbohydr Res 2011; 346:1842-7. [DOI: 10.1016/j.carres.2011.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 05/14/2011] [Accepted: 05/27/2011] [Indexed: 11/19/2022]
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16
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Kumar V. Identification of the sequence motif of glycoside hydrolase 13 family members. Bioinformation 2011; 6:61-3. [PMID: 21544166 PMCID: PMC3082856 DOI: 10.6026/97320630006061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/07/2011] [Indexed: 11/23/2022] Open
Abstract
A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the -1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 family members.
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Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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17
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Kumar V. Identification of the conserved spatial position of key active-site atoms in glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:1564-9. [PMID: 20557875 DOI: 10.1016/j.carres.2010.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 04/22/2010] [Accepted: 04/27/2010] [Indexed: 11/30/2022]
Abstract
A computational study on the glycoside hydrolase 13 (GH13) family of the CAZy database has been carried out at the atomic level in order to identify the conserved positions that may be responsible for recognition of the substrate. Analysis with substrate analog-, inhibitor-, or product-bound 3D structures was carried out to find the atomic spatial arrangement of the amino acids that make -2, -1, +1, and +2 subsites and water oxygen atoms around the ligand. The identified conserved positions of subsites were independent from the nature of the amino acid. The -1 and +1 subsites have more conserved positions than the -2 and +2 subsites. Some of the clusters of the -1 and +1 subsites have atoms of the same chemical nature. A spatially conserved position for water, which is stabilized by a hydrogen bond with the carboxyl group of a proton donor (Glu) and Asp of the catalytic triad, was found in the -1 subsite of 75% of the enzymes subjected to analysis. This position could be the region of hydrolytic water.
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Affiliation(s)
- Vikash Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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18
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Analysis of the key active subsites of glycoside hydrolase 13 family members. Carbohydr Res 2010; 345:893-8. [DOI: 10.1016/j.carres.2010.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 02/07/2010] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
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19
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Yang SJ, Min BC, Kim YW, Jang SM, Lee BH, Park KH. Changes in the catalytic properties of Pyrococcus furiosus thermostable amylase by mutagenesis of the substrate binding sites. Appl Environ Microbiol 2007; 73:5607-12. [PMID: 17630303 PMCID: PMC2042082 DOI: 10.1128/aem.00499-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrococcus furiosus thermostable amylase (TA) is a cyclodextrin (CD)-degrading enzyme with a high preference for CDs over maltooligosaccharides. In this study, we investigated the roles of four residues (His414, Gly415, Met439, and Asp440) in the function of P. furiosus TA by using site-directed mutagenesis and kinetic analysis. A variant form of P. furiosus TA containing two mutations (H414N and G415E) exhibited strongly enhanced alpha-(1,4)-transglycosylation activity, resulting in the production of a series of maltooligosaccharides that were longer than the initial substrates. In contrast, the variant enzymes with single mutations (H414N or G415E) showed a substrate preference similar to that of the wild-type enzyme. Other mutations (M439W and D440H) reversed the substrate preference of P. furiosus TA from CDs to maltooligosaccharides. Relative substrate preferences for maltoheptaose over beta-CD, calculated by comparing k(cat)/K(m) ratios, of 1, 8, and 26 for wild-type P. furiosus TA, P. furiosus TA with D440H, and P. furiosus TA with M439W and D440H, respectively, were found. Our results suggest that His414, Gly415, Met439, and Asp440 play important roles in substrate recognition and transglycosylation. Therefore, this study provides information useful in engineering glycoside hydrolase family 13 enzymes.
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Affiliation(s)
- Sung-Jae Yang
- Center for Agricultural Biomaterials and Department of Food Science and Biotechnology, Seoul National University, Sillim-dong, Kwanak-gu, Seoul 151-921, Korea
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