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Pijning T, Dijkhuizen L. Unprecedented Diversity of the Glycoside Hydrolase Family 70: A Comprehensive Analysis of Sequence, Structure, and Function. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16911-16929. [PMID: 39025827 PMCID: PMC11299179 DOI: 10.1021/acs.jafc.4c04807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
The glycoside hydrolase family 70 (GH70) contains bacterial extracellular multidomain enzymes, synthesizing α-glucans from sucrose or starch-like substrates. A few dozen have been biochemically characterized, while crystal structures cover only the core domains and lack significant parts of auxiliary domains. Here we present a systematic overview of GH70 enzymes and their 3D structural organization and bacterial origin. A representative set of 234 permuted and 25 nonpermuted GH70 enzymes was generated, covering 12 bacterial families and 3 phyla and containing 185 predicted glucansucrases (GS), 15 branching sucrases (BrS), 8 "twin" GS-BrSs, and 51 α-glucanotransferases (α-GT). Analysis of AlphaFold models of all 259 entries showed that, apart from the core domains, the structural variation regarding auxiliary domains is far greater than anticipated, with nine different domain types. We analyzed the phylogenetic distribution and discuss the possible roles of auxiliary domains as well as possible correlations between enzyme specificity, auxiliary domain type, and bacterial origin.
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Affiliation(s)
- Tjaard Pijning
- Biomolecular
X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
- CarbExplore
Research B.V., Zernikelaan
8, Groningen 9747 AA, The Netherlands
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2
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Chen Z, Chen J, Huang Z, Ni D, Tian Y, Mu W. Mutations in the Different Residues between Dextransucrase Gtf-DSM and Reuteransucrase GtfO for the Investigation of Linkage Specificity Determinants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12107-12116. [PMID: 36124907 DOI: 10.1021/acs.jafc.2c04562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The dextransucrase Gtf-DSM has 99.3% sequence identity with the reuteransucrase GtfO, and only 11 out of 1045 residues are different between their N-terminally truncated recombinant forms. Gtf-DSM is capable of synthesizing a dextran with 1% (α1 → 2), 6% (α1 → 4), 24% (α1 → 3), and 69% (α1 → 6) linkages, while GtfO produces a reuteran with 21% (α1 → 6) and 79% (α1 → 4) linkages. In this work, using recombinant Gtf-DSM and GtfO as templates, parallel substitutions targeting these 11 distinguishing residues were performed to investigate their linkage specificity determinants. The combinatorial mutation (I937L/D977A/D1083V/Q1086K/K1087G) at the acceptor binding subsites +1 and +2 nearly converted the linkage specificity of Gtf-DSM to that of GtfO. Surprisingly, all of the individual or combinatorial mutations in four residues from domains IV and V of Gtf-DSM significantly altered the linkage specificity of Gtf-DSM. Additionally, all mutations in the 11 distinguishing residues of Gtf-DSM resulted in a dramatically reduced transferase/hydrolysis activity ratio, which was closer to that of GtfO. These mutation results suggested that the linkage specificity differences between Gtf-DSM and GtfO are determined by the distinct micro-physicochemical environments, formed by the concerted action of a series of residues not only from the acceptor binding subsites +1 and +2 but also from domains IV and V.
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Affiliation(s)
- Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jiajun Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuqing Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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3
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Sharma U, Vadon-Le Goff S, Harlos K, Zhao Y, Mariano N, Bijakowski C, Bourhis JM, Moali C, Hulmes DJS, Aghajari N. Dynamics of the secreted frizzled related protein Sizzled and potential implications for binding to bone morphogenetic protein-1 (BMP-1). Sci Rep 2022; 12:14850. [PMID: 36050373 PMCID: PMC9437010 DOI: 10.1038/s41598-022-18795-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022] Open
Abstract
Sizzled (Szl) is both a secreted frizzled related protein (sFRP) and a naturally occurring inhibitor of the zinc metalloproteinase bone morphogenetic protein-1 (BMP-1), a key regulator of extracellular matrix assembly and growth factor activation. Here we present a new crystal structure for Szl which differs from that previously reported by a large scale (90°) hinge rotation between its cysteine-rich and netrin-like domains. We also present results of a molecular docking analysis showing interactions likely to be involved in the inhibition of BMP-1 activity by Szl. When compared with known structures of BMP-1 in complex with small molecule inhibitors, this reveals features that may be helpful in the design of new inhibitors to prevent the excessive accumulation of extracellular matrix that is the hallmark of fibrotic diseases.
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Affiliation(s)
- Urvashi Sharma
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
- National Institute of Biologicals, A-32, Institutional Area, Sector 62, Noida, 201309, India
| | - Sandrine Vadon-Le Goff
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Karl Harlos
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Yuguang Zhao
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Natacha Mariano
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Cecile Bijakowski
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Jean-Marie Bourhis
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Catherine Moali
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - David J S Hulmes
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS-University of Lyon, 7 passage du Vercors, 69367, Lyon, France.
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4
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Jiang Y, Li X, Pijning T, Bai Y, Dijkhuizen L. Mutations in Amino Acid Residues of Limosilactobacillus reuteri 121 GtfB 4,6-α-Glucanotransferase that Affect Reaction and Product Specificity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1952-1961. [PMID: 35129339 DOI: 10.1021/acs.jafc.1c07618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Limosilactobacillus reuteri 121 4,6-α-glucanotransferase (Lr121 4,6-α-GTase), belonging to the glycosyl hydrolase (GH) 70 GtfB subfamily, converts starch and maltodextrins into linear isomalto/malto polysaccharides (IMMPs) with consecutive (α1 → 6) linkages. The recent elucidation of its crystal structure allowed identification and analysis of further structural features that determine its reaction and product specificity. Herein, sequence alignments between GtfB enzymes with different product linkage specificities (4,6-α-GTase and 4,3-α-GTase) identified amino acid residues in GH70 homology motifs, which may be critical for reaction and product specificity. Based on these alignments, four Lr121 GtfB-ΔN mutants (I1020M, S1057P, H1056G, and Q1126I) were constructed. Compared to wild-type Lr121 GtfB-ΔN, mutants S1057P and Q1126I had considerably improved catalytic efficiencies. Mutants H1056G and Q1126I showed a 9% decrease and an 11% increase, respectively, in the ratio of (α1 → 6) over (α1 → 4) linkages in maltodextrin-derived products. A change in linkage type (e.g., (α1 → 6) linkages to (α1 → 3) linkages) was not observed. The possible functional roles of these Lr121 GtfB-ΔN residues located around the acceptor substrate-binding subsites are discussed. The results provide new insights into structural determinants of the reaction and product specificity of Lr121 GtfB 4,6-α-GTase.
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Affiliation(s)
- Yawen Jiang
- State Key laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Xiaoxiao Li
- State Key laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Tjaard Pijning
- Biomolecular X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yuxiang Bai
- State Key laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, Jiangsu Province, China
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- CarbExplore Research B.V., 9747 AA Groningen, The Netherlands
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5
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Molina M, Cioci G, Moulis C, Séverac E, Remaud-Siméon M. Bacterial α-Glucan and Branching Sucrases from GH70 Family: Discovery, Structure-Function Relationship Studies and Engineering. Microorganisms 2021; 9:microorganisms9081607. [PMID: 34442685 PMCID: PMC8398850 DOI: 10.3390/microorganisms9081607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/12/2023] Open
Abstract
Glucansucrases and branching sucrases are classified in the family 70 of glycoside hydrolases. They are produced by lactic acid bacteria occupying very diverse ecological niches (soil, buccal cavity, sourdough, intestine, dairy products, etc.). Usually secreted by their producer organisms, they are involved in the synthesis of α-glucans from sucrose substrate. They contribute to cell protection while promoting adhesion and colonization of different biotopes. Dextran, an α-1,6 linked linear α-glucan, was the first microbial polysaccharide commercialized for medical applications. Advances in the discovery and characterization of these enzymes have remarkably enriched the available diversity with new catalysts. Research into their molecular mechanisms has highlighted important features governing their peculiarities thus opening up many opportunities for engineering these catalysts to provide new routes for the transformation of sucrose into value-added molecules. This article reviews these different aspects with the ambition to show how they constitute the basis for promising future developments.
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Claverie M, Cioci G, Vuillemin M, Bondy P, Remaud-Simeon M, Moulis C. Processivity of dextransucrases synthesizing very-high-molar-mass dextran is mediated by sugar-binding pockets in domain V. J Biol Chem 2020; 295:5602-5613. [PMID: 32161118 PMCID: PMC7186162 DOI: 10.1074/jbc.ra119.011995] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/30/2020] [Indexed: 11/06/2022] Open
Abstract
The dextransucrase DSR-OK from the Gram-positive bacterium Oenococcus kitaharae DSM17330 produces a dextran of the highest molar mass reported to date (∼109 g/mol). In this study, we selected a recombinant form, DSR-OKΔ1, to identify molecular determinants involved in the sugar polymerization mechanism and that confer its ability to produce a very-high-molar-mass polymer. In domain V of DSR-OK, we identified seven putative sugar-binding pockets characteristic of glycoside hydrolase 70 (GH70) glucansucrases that are known to be involved in glucan binding. We investigated their role in polymer synthesis through several approaches, including monitoring of dextran synthesis, affinity assays, sugar binding pocket deletions, site-directed mutagenesis, and construction of chimeric enzymes. Substitution of only two stacking aromatic residues in two consecutive sugar-binding pockets (variant DSR-OKΔ1-Y1162A-F1228A) induced quasi-complete loss of very-high-molar-mass dextran synthesis, resulting in production of only 10-13 kg/mol polymers. Moreover, the double mutation completely switched the semiprocessive mode of DSR-OKΔ1 toward a distributive one, highlighting the strong influence of these pockets on enzyme processivity. Finally, the position of each pocket relative to the active site also appeared to be important for polymer elongation. We propose that sugar-binding pockets spatially closer to the catalytic domain play a major role in the control of processivity. A deep structural characterization, if possible with large-molar-mass sugar ligands, would allow confirming this hypothesis.
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Affiliation(s)
- Marion Claverie
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Gianluca Cioci
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marlène Vuillemin
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Pauline Bondy
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Magali Remaud-Simeon
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Claire Moulis
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France.
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7
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Zhao B, Du R, Wang J, Xu M, Han Y, Han X, Zhou Z. Purification and biochemical characterization of a novel glucansucrase from Leuconostoc citreum B-2. Biotechnol Lett 2020; 42:1535-1545. [DOI: 10.1007/s10529-020-02881-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/31/2020] [Indexed: 01/02/2023]
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8
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Wangpaiboon K, Pitakchatwong C, Panpetch P, Charoenwongpaiboon T, Field RA, Pichyangkura R. Modified properties of alternan polymers arising from deletion of SH3-like motifs in Leuconostoc citreum ABK-1 alternansucrase. Carbohydr Polym 2019; 220:103-109. [PMID: 31196527 DOI: 10.1016/j.carbpol.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/01/2019] [Accepted: 05/01/2019] [Indexed: 01/20/2023]
Abstract
Alternansucrase (ALT, EC 2.4.1.140) catalyses the formation of an alternating 〈-1, 3/1, 6-linked glucan, with periodic branch points, from sucrose substrate. Beyond the catalytic domain, this enzyme harbours seven additional C-terminal SH3-like repeats. We herein generated two truncated alternansucrases, possessing deletions of three and seven adjacent SH3 motifs, giving Δ3SHALT and Δ7SHALT. Δ3SHALT and Δ7SHALT exhibited kcat/Km for transglycosylation activity 2.3- and 1.5-fold lower than wild-type ALT (WTALT), while hydrolysis was detected only in the truncated ALTs, oligosaccharide patterns and polymer glycosidic linkage were similar to that of WTALT. The viscosities of ALT polymers increase by ˜100-fold at 15% (w/v), with gel-like states formed at 12.5, 15.0, and 20.0% (w/v) produced by polymer from WTALT, Δ3SHALT, and Δ7SHALT, respectively. The average nanoparticle sizes of Δ3SHALT and Δ7SHALT polymers were 80 nm, compared to 90 nm from WTALT. In conclusion, even relatively subtle differences in the structure of ALT-produced alternan give rise to profound impact on the glucan polymer physicochemical properties.
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Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Pawinee Panpetch
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Molina M, Moulis C, Monties N, Pizzut-Serin S, Guieysse D, Morel S, Cioci G, Remaud-Siméon M. Deciphering an Undecided Enzyme: Investigations of the Structural Determinants Involved in the Linkage Specificity of Alternansucrase. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04510] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manon Molina
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Claire Moulis
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Nelly Monties
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Sandra Pizzut-Serin
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - David Guieysse
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Sandrine Morel
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Gianluca Cioci
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
| | - Magali Remaud-Siméon
- LISBP (Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés), Université de Toulouse, CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), INSA (Institut National des Sciences Appliquées), F-31077 Toulouse, France
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10
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Osorio MI, Zúñiga MA, Mendoza F, Jaña GA, Jiménez VA. Modulation of glucan-enzyme interactions by domain V in GTF-SI from Streptococcus mutans. Proteins 2018; 87:74-80. [PMID: 30367507 DOI: 10.1002/prot.25624] [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: 07/05/2018] [Revised: 09/27/2018] [Accepted: 10/16/2018] [Indexed: 11/10/2022]
Abstract
Glucansucrase GTF-SI from Streptococcus mutans is a multidomain enzyme that catalyzes the synthesis of glucan polymers. Domain V locates 100 Å from the catalytic site and is required for an optimal activity. Nevertheless, the mechanism governing its functional role remains elusive. In this work, homology modeling and molecular dynamics simulations were employed to examine the effect of domain V in the structure and glucan-binding ability of GTF-SI in full and truncated enzyme models. Our results showed that domain V increases the flexibility of the α4'-loop-α4″ motif near the catalytic site resulting in a higher surface for glucan association, and modulates the orientation of a growing oligosaccharide (N=8-23) in glucan-enzyme complexes towards engaging in favorable contacts throughout the protein, whereas in the truncated model the glucan protrudes randomly from domain B towards the solvent. These results are valuable to increase understanding about the functional role of domain V in GH70 glucansucrases.
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Affiliation(s)
- Manuel I Osorio
- Fisicoquímica Molecular, Universidad Andres Bello, Santiago, Chile.,Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Talcahuano, Chile
| | - Matías A Zúñiga
- Fisicoquímica Molecular, Universidad Andres Bello, Santiago, Chile.,Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Talcahuano, Chile
| | - Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Talcahuano, Chile
| | - Gonzalo A Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Talcahuano, Chile
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Talcahuano, Chile
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11
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Ben Imeddourene A, Esque J, André I. Combining multi-scale modelling methods to decipher molecular motions of a branching sucrase from glycoside-hydrolase family 70. PLoS One 2018; 13:e0201323. [PMID: 30067837 PMCID: PMC6070258 DOI: 10.1371/journal.pone.0201323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/12/2018] [Indexed: 01/23/2023] Open
Abstract
Among α-transglucosylases from Glycoside-Hydrolase family 70, the ΔN123-GB-CD2 enzyme derived from the bifunctional DSR-E from L. citreum NRRL B-1299 is particularly interesting as it was the first described engineered Branching Sucrase, not able to elongate glucan polymers from sucrose substrate. The previously reported overall structural organization of this multi-domain enzyme is an intricate U-shape fold conserved among GH70 enzymes which showed a certain conformational variability of the so-called domain V, assumed to play a role in the control of product structures, in available X-ray structures. Understanding the role of functional dynamics on enzyme reaction and substrate recognition is of utmost interest although it remains a challenge for biophysical methods. By combining long molecular dynamics simulation (1μs) and multiple analyses (NMA, PCA, Morelet Continuous Wavelet Transform and Cross Correlations Dynamics), we investigated here the dynamics of ΔN123-GB-CD2 alone and in interaction with sucrose substrate. Overall, our results provide the detailed picture at atomic level of the hierarchy of motions occurring along different timescales and how they are correlated, in agreement with experimental structural data. In particular, detailed analysis of the different structural domains revealed cooperative dynamic behaviors such as twisting, bending and wobbling through anti- and correlated motions, and also two structural hinge regions, of which one was unreported. Several highly flexible loops surrounding the catalytic pocket were also highlighted, suggesting a potential role in the acceptor promiscuity of ΔN123-GBD-CD2. Normal modes and essential dynamics underlined an interesting two-fold dynamic of the catalytic domain A, pivoting about an axis splitting the catalytic gorge in two parts. The comparison of the conformational free energy landscapes using principal component analysis of the enzyme in absence or in presence of sucrose, also revealed a more harmonic basin when sucrose is bound with a shift population of the bending mode, consistent with the substrate binding event.
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Affiliation(s)
- Akli Ben Imeddourene
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jérémy Esque
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
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12
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Gangoiti J, Pijning T, Dijkhuizen L. Biotechnological potential of novel glycoside hydrolase family 70 enzymes synthesizing α-glucans from starch and sucrose. Biotechnol Adv 2017; 36:196-207. [PMID: 29133008 DOI: 10.1016/j.biotechadv.2017.11.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/24/2017] [Accepted: 11/06/2017] [Indexed: 11/18/2022]
Abstract
Transglucosidases belonging to the glycoside hydrolase (GH) family 70 are promising enzymatic tools for the synthesis of α-glucans with defined structures from renewable sucrose and starch substrates. Depending on the GH70 enzyme specificity, α-glucans with different structures and physicochemical properties are produced, which have found diverse (potential) commercial applications, e.g. in food, health and as biomaterials. Originally, the GH70 family was established only for glucansucrase enzymes of lactic acid bacteria that catalyze the synthesis of α-glucan polymers from sucrose. In recent years, we have identified 3 novel subfamilies of GH70 enzymes (designated GtfB, GtfC and GtfD), inactive on sucrose but converting starch/maltodextrin substrates into novel α-glucans. These novel starch-acting enzymes considerably enlarge the panel of α-glucans that can be produced. They also represent very interesting evolutionary intermediates between sucrose-acting GH70 glucansucrases and starch-acting GH13 α-amylases. Here we provide an overview of the repertoire of GH70 enzymes currently available with focus on these novel starch-acting GH70 enzymes and their biotechnological potential. Moreover, we discuss key developments in the understanding of structure-function relationships of GH70 enzymes in the light of available three-dimensional structures, and the protein engineering strategies that were recently applied to expand their natural product specificities.
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Affiliation(s)
- Joana Gangoiti
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tjaard Pijning
- Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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13
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Claverie M, Cioci G, Vuillemin M, Monties N, Roblin P, Lippens G, Remaud-Simeon M, Moulis C. Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02182] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Marion Claverie
- LISBP, Université de Toulouse, CNRS, INRA,
INSA, Toulouse, France
| | - Gianluca Cioci
- LISBP, Université de Toulouse, CNRS, INRA,
INSA, Toulouse, France
| | | | - Nelly Monties
- LISBP, Université de Toulouse, CNRS, INRA,
INSA, Toulouse, France
| | - Pierre Roblin
- Université de Toulouse, LGC UMR 5503 (CNRS/UPS/INPT), 118 route de Narbonne 31062 Toulouse, France
| | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA,
INSA, Toulouse, France
| | | | - Claire Moulis
- LISBP, Université de Toulouse, CNRS, INRA,
INSA, Toulouse, France
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14
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Moulis C, André I, Remaud-Simeon M. GH13 amylosucrases and GH70 branching sucrases, atypical enzymes in their respective families. Cell Mol Life Sci 2016; 73:2661-79. [PMID: 27141938 PMCID: PMC11108324 DOI: 10.1007/s00018-016-2244-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 12/22/2022]
Abstract
Amylosucrases and branching sucrases are α-retaining transglucosylases found in the glycoside-hydrolase families 13 and 70, respectively, of the clan GH-H. These enzymes display unique activities in their respective families. Using sucrose as substrate and without mediation of nucleotide-activated sugars, amylosucrase catalyzes the formation of an α-(1 → 4) linked glucan that resembles amylose. In contrast, the recently discovered branching sucrases are unable to catalyze polymerization of glucosyl units as they are rather specific for dextran branching through α-(1 → 2) or α-(1 → 3) branching linkages depending on the enzyme regiospecificity. In addition, GH13 amylosucrases and GH70 branching sucrases are naturally promiscuous and can glucosylate different types of acceptor molecules including sugars, polyols, or flavonoids. Amylosucrases have been the most investigated glucansucrases, in particular to control product profiles or to successfully develop tailored α-transglucosylases able to glucosylate various molecules of interest, for example, chemically protected carbohydrates that are planned to enter in chemoenzymatic pathways. The structural traits of these atypical enzymes will be described and compared, and an overview of the potential of natural or engineered enzymes for glycodiversification and chemoenzymatic synthesis will be highlighted.
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Affiliation(s)
- Claire Moulis
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077, Toulouse, France
- CNRS, UMR5504, 31400, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400, Toulouse, France
| | - Isabelle André
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077, Toulouse, France
- CNRS, UMR5504, 31400, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400, Toulouse, France
| | - Magali Remaud-Simeon
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077, Toulouse, France.
- CNRS, UMR5504, 31400, Toulouse, France.
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400, Toulouse, France.
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15
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Meng X, Gangoiti J, Bai Y, Pijning T, Van Leeuwen SS, Dijkhuizen L. Structure-function relationships of family GH70 glucansucrase and 4,6-α-glucanotransferase enzymes, and their evolutionary relationships with family GH13 enzymes. Cell Mol Life Sci 2016; 73:2681-706. [PMID: 27155661 PMCID: PMC4919382 DOI: 10.1007/s00018-016-2245-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/13/2022]
Abstract
Lactic acid bacteria (LAB) are known to produce large amounts of α-glucan exopolysaccharides. Family GH70 glucansucrase (GS) enzymes catalyze the synthesis of these α-glucans from sucrose. The elucidation of the crystal structures of representative GS enzymes has advanced our understanding of their reaction mechanism, especially structural features determining their linkage specificity. In addition, with the increase of genome sequencing, more and more GS enzymes are identified and characterized. Together, such knowledge may promote the synthesis of α-glucans with desired structures and properties from sucrose. In the meantime, two new GH70 subfamilies (GTFB- and GTFC-like) have been identified as 4,6-α-glucanotransferases (4,6-α-GTs) that represent novel evolutionary intermediates between the family GH13 and "classical GH70 enzymes". These enzymes are not active on sucrose; instead, they use (α1 → 4) glucans (i.e. malto-oligosaccharides and starch) as substrates to synthesize novel α-glucans by introducing linear chains of (α1 → 6) linkages. All these GH70 enzymes are very interesting biocatalysts and hold strong potential for applications in the food, medicine and cosmetic industries. In this review, we summarize the microbiological distribution and the structure-function relationships of family GH70 enzymes, introduce the two newly identified GH70 subfamilies, and discuss evolutionary relationships between family GH70 and GH13 enzymes.
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Affiliation(s)
- Xiangfeng Meng
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Joana Gangoiti
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Yuxiang Bai
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Tjaard Pijning
- Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Sander S Van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
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16
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Effect of a single point mutation on the interaction of glucans with a glucansucrase from Leuconostoc mesenteroides NRRL B-1118. Carbohydr Res 2016; 428:57-61. [PMID: 27131127 DOI: 10.1016/j.carres.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/01/2016] [Accepted: 04/08/2016] [Indexed: 11/22/2022]
Abstract
Our previous work showed that substitution of an amino acid that is coupled with the +2 subsite adjacent to the transition stabilizer of a glucansucrase, which produces a water-insoluble glucan, resulted in significant changes in the structures and yields of the water-insoluble glucans produced. We now describe how these changes affect the ability of the glucansucrase to bind to exogenous glucans, and how these glucans can influence the yield, product structures, and kinetics of the mutant glucansucrases. The activity of the wild-type enzyme, with threonine at position 654, is not significantly activated by added dextran, and the yield of water-insoluble glucan from sucrose is only slightly increased by dextran. Mutant T654Y is not affected at all by the addition of dextran. However, several mutant enzymes exhibit markedly lower yields of glucan relative to the wild type; these lower yields can be partially or completely overcome by the addition of water-soluble dextran. Although evidence indicates that the soluble dextran is incorporated into water-insoluble glucan, the increased yields cannot be accounted for solely by incorporation of the dextran into insoluble product. Furthermore, these DsrI mutants are significantly activated by exogenous glucans. The addition of dextran does not markedly change the KM for sucrose in the mutant enzymes, but does increase the Vmax of the reaction. These effects apparently depend on the presence of unbranched sequences of α1→6-linked D-glucose units in the glucan.
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17
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Brison Y, Malbert Y, Czaplicki G, Mourey L, Remaud-Simeon M, Tranier S. Structural Insights into the Carbohydrate Binding Ability of an α-(1→2) Branching Sucrase from Glycoside Hydrolase Family 70. J Biol Chem 2016; 291:7527-40. [PMID: 26865636 DOI: 10.1074/jbc.m115.688796] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 11/06/2022] Open
Abstract
The α-(1→2) branching sucrase ΔN123-GBD-CD2 is a transglucosylase belonging to glycoside hydrolase family 70 (GH70) that catalyzes the transfer ofd-glucosyl units from sucroseto dextrans or gluco-oligosaccharides via the formation of α-(1→2) glucosidic linkages. The first structures of ΔN123-GBD-CD2 in complex withd-glucose, isomaltosyl, or isomaltotriosyl residues were solved. The glucose complex revealed three glucose-binding sites in the catalytic gorge and six additional binding sites at the surface of domains B, IV, and V. Soaking with isomaltotriose or gluco-oligosaccharides led to structures in which isomaltosyl or isomaltotriosyl residues were found in glucan binding pockets located in domain V. One aromatic residue is systematically identified at the bottom of these pockets in stacking interaction with one glucosyl moiety. The carbohydrate is also maintained by a network of hydrogen bonds and van der Waals interactions. The sequence of these binding pockets is conserved and repeatedly present in domain V of several GH70 glucansucrases known to bind α-glucans. These findings provide the first structural evidence of the molecular interaction occurring between isomalto-oligosaccharides and domain V of the GH70 enzymes.
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Affiliation(s)
- Yoann Brison
- the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Yannick Malbert
- the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, the CNRS, UMR5504, F-31400 Toulouse
| | - Georges Czaplicki
- the Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 route de Narbonne, BP 64182, F-31077, Toulouse, and the Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Lionel Mourey
- the Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 route de Narbonne, BP 64182, F-31077, Toulouse, and the Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
| | - Magali Remaud-Simeon
- the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, the INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, the CNRS, UMR5504, F-31400 Toulouse,
| | - Samuel Tranier
- the Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique (CNRS), 205 route de Narbonne, BP 64182, F-31077, Toulouse, and the Université de Toulouse, Université Paul Sabatier, IPBS, F-31077 Toulouse, France
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18
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Secreted expression of Leuconostoc mesenteroides glucansucrase in Lactococcus lactis for the production of insoluble glucans. Appl Microbiol Biotechnol 2015; 99:10001-10. [DOI: 10.1007/s00253-015-6854-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 02/03/2023]
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19
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Meng X, Dobruchowska JM, Pijning T, Gerwig GJ, Kamerling JP, Dijkhuizen L. Truncation of domain V of the multidomain glucansucrase GTF180 of Lactobacillus reuteri 180 heavily impairs its polysaccharide-synthesizing ability. Appl Microbiol Biotechnol 2015; 99:5885-94. [PMID: 25586581 DOI: 10.1007/s00253-014-6361-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 12/17/2014] [Accepted: 12/20/2014] [Indexed: 01/23/2023]
Abstract
Glucansucrases are exclusively found in lactic acid bacteria and synthesize a variety of α-glucans from sucrose. They are large multidomain enzymes belonging to the CAZy family 70 of glycoside hydrolase enzymes (GH70). The crystal structure of the N-terminal truncated GTF180 of Lactobacillus reuteri 180 (GTF180-ΔN) revealed that the polypeptide chain follows a U shape course to form five domains, including domains A, B, and C, which resemble those of family GH13 enzymes, and two extra and novel domains (domains IV and V), which are attached to the catalytic core. To elucidate the functional roles of domain V, we have deleted the domain V fragments from both the N- and C-terminal ends (GTF180-ΔNΔV). Truncation of domain V of GTF180-ΔN yielded a catalytically fully active enzyme but with heavily impaired polysaccharide synthesis ability. Instead, GTF180-ΔNΔV produced a large amount of oligosaccharides. Domain V is not involved in determining the linkage specificity, and the size of polysaccharide produced as the polysaccharide produced by GTF180-ΔNΔV was identical in size and structure with that of GTF180-ΔN. The data indicates that GTF180-ΔNΔV acts nonprocessively, frequently initiating synthesis of a new oligosaccharide from sucrose, instead of continuing the synthesis of a full size polysaccharide. Mutations L940E and L940F in GTF180-ΔNΔV, which are involved in the acceptor substrate binding, restored polysaccharide synthesis almost to the level of GTF180-ΔN. These results demonstrated that interactions of growing glucan chains with both domain V and acceptor substrate binding sites are important for polysaccharide synthesis.
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Affiliation(s)
- Xiangfeng Meng
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
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