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Structure and function of microbial α-l-fucosidases: a mini review. Essays Biochem 2023; 67:399-414. [PMID: 36805644 PMCID: PMC10154630 DOI: 10.1042/ebc20220158] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.
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Wu MH, Kao MR, Li CW, Yu SM, Ho THD. A unique self-truncation of bacterial GH5 endoglucanases leads to enhanced activity and thermostability. BMC Biol 2022; 20:137. [PMID: 35681203 PMCID: PMC9185962 DOI: 10.1186/s12915-022-01334-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background β-1,4-endoglucanase (EG) is one of the three types of cellulases used in cellulose saccharification during lignocellulosic biofuel/biomaterial production. GsCelA is an EG secreted by the thermophilic bacterium Geobacillus sp. 70PC53 isolated from rice straw compost in southern Taiwan. This enzyme belongs to glycoside hydrolase family 5 (GH5) with a TIM-barrel structure common among all members of this family. GsCelA exhibits excellent lignocellulolytic activity and thermostability. In the course of investigating the regulation of this enzyme, it was fortuitously discovered that GsCelA undergoes a novel self-truncation/activation process that appears to be common among GH5 enzymes. Results Three diverse Gram-positive bacterial GH5 EGs, but not a GH12 EG, undergo an unexpected self-truncation process by removing a part of their C-terminal region. This unique process has been studied in detail with GsCelA. The purified recombinant GsCelA was capable of removing a 53-amino-acid peptide from the C-terminus. Natural or engineered GsCelA truncated variants, with up to 60-amino-acid deletion from the C-terminus, exhibited higher specific activity and thermostability than the full-length enzyme. Interestingly, the C-terminal part that is removed in this self-truncation process is capable of binding to cellulosic substrates of EGs. The protein truncation, which is pH and temperature dependent, occurred between amino acids 315 and 316, but removal of these two amino acids did not stop the process. Furthermore, mutations of E142A and E231A, which are essential for EG activity, did not affect the protein self-truncation process. Conversely, two single amino acid substitution mutations affected the self-truncation activity without much impact on EG activities. In Geobacillus sp. 70PC53, the full-length GsCelA was first synthesized in the cell but progressively transformed into the truncated form and eventually secreted. The GsCelA self-truncation was not affected by standard protease inhibitors, but could be suppressed by EDTA and EGTA and enhanced by certain divalent ions, such as Ca2+, Mg2+, and Cu2+. Conclusions This study reveals novel insights into the strategy of Gram-positive bacteria for directing their GH5 EGs to the substrate, and then releasing the catalytic part for enhanced activity via a spontaneous self-truncation process. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01334-y.
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Affiliation(s)
- Mei-Huey Wu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China.,Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China. .,Biotechnology Research Center, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China. .,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China.
| | - Tuan-Hua David Ho
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan, Republic of China. .,Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan, Republic of China. .,Biotechnology Research Center, National Chung Hsing University, Taichung, 402, Taiwan, Republic of China.
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Cha JH, Hong M, Cha CJ. Fungal β-Glycosidase Belonging to Subfamily 4 of Glycoside Hydrolase Family 30 with Transglycosylation Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15261-15267. [PMID: 34879649 DOI: 10.1021/acs.jafc.1c05197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fomitopsis palustris, a prominent wood decayer, is known to produce a variety of glycoside hydrolases (GHs). In this study, we characterized a fungal β-glycosidase belonging to subfamily 4 of GH family 30 (GH30). The recombinant protein (FpGH30) showed the highest hydrolytic activity toward p-nitrophenyl-β-d-fucopyranoside (pNPβFuc), followed by p-nitrophenyl-α-l-arabinopyranoside (pNPαAra) and p-nitrophenyl-β-d-galactopyranoside (pNPβGal). FpGH30 also exhibited transglycosylation activities, which catalyzed the transfer of glycosyl moieties to different glycosides and alkyl alcohols. When pNPβFuc, pNPβGal, and pNPαAra were used as substrates, self-condensation reactions occurred, leading to the production of the corresponding transglycosylated products with yields of 21, 26, and 25%, respectively. The enzyme was also able to catalyze the transfucosylation of pNP derivatives of β-d-glucose, β-d-mannose, and β-d-xylose and alkyl alcohols (C1-C6), producing the corresponding transfucosylated products and alkyl fucosides. Our study indicates that FpGH30 is the first characterized fungal β-glycosidase belonging to subfamily 4 of GH30 with transglycosylation activities.
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Affiliation(s)
- Ju-Hee Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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Glycoside Hydrolase family 30 harbors fungal subfamilies with distinct polysaccharide specificities. N Biotechnol 2021; 67:32-41. [PMID: 34952234 DOI: 10.1016/j.nbt.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/19/2021] [Accepted: 12/19/2021] [Indexed: 11/21/2022]
Abstract
Efficient bioconversion of agro-industrial side streams requires a wide range of enzyme activities. Glycoside Hydrolase family 30 (GH30) is a diverse family that contains various catalytic functions and has so far been divided into ten subfamilies (GH30_1-10). In this study, a GH30 phylogenetic tree using over 150 amino acid sequences was contructed. The members of GH30 cluster into four subfamilies and eleven candidates from these subfamilies were selected for biochemical characterization. Novel enzyme activities were identified in GH30. GH30_3 enzymes possess β-(1→6)-glucanase activity. GH30_5 targets β-(1→6)-galactan with mainly β-(1→6)-galactobiohydrolase catalytic behavior. β-(1→4)-Xylanolytic enzymes belong to GH30_7 targeting β-(1→4)-xylan with several activities (e.g. xylobiohydrolase, endoxylanase). Additionally, a new fungal subfamily in GH30 was proposed, i.e. GH30_11, which displays β-(1→6)-galactobiohydrolase. This study confirmed that GH30 fungal subfamilies harbor distinct polysaccharide specificity and have high potential for the production of short (non-digestible) di- and oligosaccharides.
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Korczynska M, Xiang DF, Zhang Z, Xu C, Narindoshvili T, Kamat SS, Williams HJ, Chang SS, Kolb P, Hillerich B, Sauder JM, Burley SK, Almo SC, Swaminathan S, Shoichet BK, Raushel FM. Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. Biochemistry 2014; 53:4727-38. [PMID: 24955762 PMCID: PMC4108184 DOI: 10.1021/bi500595c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A novel lactonase from Mycoplasma synoviae 53 (MS53_0025) and Mycoplasma agalactiae PG2 (MAG_6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53_0025 was determined to a resolution of 2.06 Å. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53_0025 and MAG_6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 10(4) and 5.7 × 10(4) M(-1) s(-1) and l-arabino-1,4-lactone-5-phosphate (7) with kcat/Km values of 1.3 × 10(4) and 2.2 × 10(4) M(-1) s(-1), respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.
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Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2330, United States
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Biochemical and mutational analyses of a multidomain cellulase/mannanase from Caldicellulosiruptor bescii. Appl Environ Microbiol 2012; 78:2230-40. [PMID: 22247178 DOI: 10.1128/aem.06814-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of Caldicellulosiruptor bescii Cel9B/Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of C. bescii, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydrate-binding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/Man5A were assigned to the N- and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ∼5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s(-1) ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent k(cat) of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the K(m) led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.
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