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Shi Q, Abdel-Hamid AM, Sun Z, Cheng Y, Tu T, Cann I, Yao B, Zhu W. Carbohydrate-binding modules facilitate the enzymatic hydrolysis of lignocellulosic biomass: Releasing reducing sugars and dissociative lignin available for producing biofuels and chemicals. Biotechnol Adv 2023; 65:108126. [PMID: 36921877 DOI: 10.1016/j.biotechadv.2023.108126] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
The microbial decomposition and utilization of lignocellulosic biomass present in the plant tissues are driven by a series of carbohydrate active enzymes (CAZymes) acting in concert. As the non-catalytic domains widely found in the modular CAZymes, carbohydrate-binding modules (CBMs) are intimately associated with catalytic domains (CDs) that effect the diverse hydrolytic reactions. The CBMs function as auxiliary components for the recognition, adhesion, and depolymerization of the complex substrate mediated by the associated CDs. Therefore, CBMs are deemed as significant biotools available for enzyme engineering, especially to facilitate the enzymatic hydrolysis of dense and insoluble plant tissues to acquire more fermentable sugars. This review aims at presenting the taxonomies and biological properties of the CBMs currently curated in the CAZy database. The molecular mechanisms that CBMs use in assisting the enzymatic hydrolysis of plant polysaccharides and the regulatory factors of CBM-substrate interactions are outlined in detail. In addition, guidelines for the rational designs of CBM-fused CAZymes are proposed. Furthermore, the potential to harness CBMs for industrial applications, especially in enzymatic pretreatment of the recalcitrant lignocellulose, is evaluated. It is envisaged that the ideas outlined herein will aid in the engineering and production of novel CBM-fused enzymes to facilitate efficient degradation of lignocellulosic biomass to easily fermentable sugars for production of value-added products, including biofuels.
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Affiliation(s)
- Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed M Abdel-Hamid
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Animal Science, University of Illinois at Urbana-Champaign, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA; Center for East Asian and Pacific Studies, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Duan X, Zhu Q, Zhang X, Shen Z, Huang Y. Expression, biochemical and structural characterization of high-specific-activity β-amylase from Bacillus aryabhattai GEL-09 for application in starch hydrolysis. Microb Cell Fact 2021; 20:182. [PMID: 34537082 PMCID: PMC8449922 DOI: 10.1186/s12934-021-01649-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND β-amylase (EC 3.2.1.2) is an exo-enzyme that shows high specificity for cleaving the α-1,4-glucosidic linkage of starch from the non-reducing end, thereby liberating maltose. In this study, we heterologously expressed and characterized a novel β-amylase from Bacillus aryabhattai. RESULTS The amino acid-sequence alignment showed that the enzyme shared the highest sequence identity with β-amylase from Bacillus flexus (80.73%) followed by Bacillus cereus (71.38%). Structural comparison revealed the existence of an additional starch-binding domain (SBD) at the C-terminus of B. aryabhattai β-amylase, which is notably different from plant β-amylases. The recombinant enzyme purified 4.7-fold to homogeneity, with a molecular weight of ~ 57.6 kDa and maximal activity at pH 6.5 and 50 °C. Notably, the enzyme exhibited the highest specific activity (3798.9 U/mg) among reported mesothermal microbial β-amylases and the highest specificity for soluble starch, followed by corn starch. Kinetic analysis showed that the Km and kcat values were 9.9 mg/mL and 116961.1 s- 1, respectively. The optimal reaction conditions to produce maltose from starch resulted in a maximal yield of 87.0%. Moreover, molecular docking suggested that B. aryabhattai β-amylase could efficiently recognize and hydrolyze maltotetraose substrate. CONCLUSIONS These results suggested that B. aryabhattai β-amylase could be a potential candidate for use in the industrial production of maltose from starch.
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Affiliation(s)
- Xuguo Duan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Qiuyu Zhu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xinyi Zhang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhenyan Shen
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Yue Huang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Azzopardi E, Lloyd C, Teixeira SR, Conlan RS, Whitaker IS. Clinical applications of amylase: Novel perspectives. Surgery 2016; 160:26-37. [PMID: 27117578 DOI: 10.1016/j.surg.2016.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 12/20/2015] [Accepted: 01/08/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Amylase was the first enzyme to be characterized, and for the previous 200 years, its clinical role has been restricted to a diagnostic aid. Recent interface research has led to a substantial expansion of its role into novel, viable diagnostic, and therapeutic applications to cancer, infection, and wound healing. This review provides a concise "state-of-the-art" overview of the genetics, structure, distribution, and localization of amylase in humans. METHOD A first-generation literature search was performed with the MeSH search string "Amylase AND (diagnost∗ OR therapeut$)" on OVIDSP and PUBMED platforms. A second-generation search was then performed by forward and backward referencing on Web of Knowledge™ and manual indexing, limited to the English Language. RESULTS "State of the Art" in amylase genetics, structure, function distribution, localisation and detection of amylase in humans is provided. To the 4 classic patterns of hyperamylasemia (pancreatic, salivary, macroamylasemia, and combinations) a fifth, the localized targeting of amylase to specific foci of infection, is proposed. CONCLUSIONS The implications are directed at novel therapeutic and diagnostic clinical applications of amylase such as the novel therapeutic drug classes capable of targeted delivery and "smart release" in areas of clinical need. Future directions of research in areas of high clinical benefit are reported.
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Affiliation(s)
- Ernest Azzopardi
- Reconstructive Surgery and Regenerative Medicine Group, Swansea University, Swansea, United Kingdom; Centre for Nanohealth, Swansea University, Swansea, United Kingdom; The Welsh Centre for Burns and Plastic Surgery, Morriston Hospital, Swansea, United Kingdom; Swansea University Medical School, Swansea University, Swansea, United Kingdom.
| | - Catherine Lloyd
- Reconstructive Surgery and Regenerative Medicine Group, Swansea University, Swansea, United Kingdom; Centre for Nanohealth, Swansea University, Swansea, United Kingdom
| | | | - R Steven Conlan
- Centre for Nanohealth, Swansea University, Swansea, United Kingdom; Swansea University Medical School, Swansea University, Swansea, United Kingdom
| | - Iain S Whitaker
- Reconstructive Surgery and Regenerative Medicine Group, Swansea University, Swansea, United Kingdom; The Welsh Centre for Burns and Plastic Surgery, Morriston Hospital, Swansea, United Kingdom; Swansea University Medical School, Swansea University, Swansea, United Kingdom
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Wilkens C, Auger KD, Anderson NT, Meekins DA, Raththagala M, Abou Hachem M, Payne CM, Gentry MS, Svensson B. Plant α‐glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose. FEBS Lett 2016; 590:118-28. [DOI: 10.1002/1873-3468.12027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Kyle D. Auger
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Nolan T. Anderson
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - David A. Meekins
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Madushi Raththagala
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology University of Kentucky Lexington KY USA
| | - Birte Svensson
- Enzyme and Protein Chemistry Department of Systems Biology Technical University of Denmark Kongens Lyngby Denmark
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Park KH, Jung JH, Park SG, Lee ME, Holden JF, Park CS, Woo EJ. Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase fromPyrococcussp. ST04. ACTA ACUST UNITED AC 2014; 70:1659-68. [DOI: 10.1107/s1399004714006567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/25/2014] [Indexed: 11/11/2022]
Abstract
A novel maltose-forming α-amylase (PSMA) was recently found in the hyperthermophilic archaeonPyrococcussp. ST04. This enzyme shows <13% amino-acid sequence identity to other known α-amylases and displays a unique enzymatic property in that it hydrolyzes both α-1,4-glucosidic and α-1,6-glucosidic linkages of substrates, recognizing only maltose units, in an exo-type manner. Here, the crystal structure of PSMA at a resolution of 1.8 Å is reported, showing a tight ring-shaped tetramer with monomers composed of two domains: an N-domain (amino acids 1–341) with a typical GH57 family (β/α)7-barrel fold and a C-domain (amino acids 342–597) composed of α-helical bundles. A small closed cavity observed in proximity to the catalytic residues Glu153 and Asp253 at the domain interface has the appropriate volume and geometry to bind a maltose unit, accounting for the selective exo-type maltose hydrolysis of the enzyme. A narrow gate at the putative subsite +1 formed by residue Phe218 and Phe452 is essential for specific cleavage of glucosidic bonds. The closed cavity at the active site is connected to a short substrate-binding channel that extends to the central hole of the tetramer, exhibiting a geometry that is significantly different from classical maltogenic amylases or β-amylases. The structural features of this novel exo-type maltose-forming α-amylase provide a molecular basis for its unique enzymatic characteristics and for its potential use in industrial applications and protein engineering.
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Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:793-802. [PMID: 24582745 DOI: 10.1016/j.bbapap.2014.02.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/27/2014] [Accepted: 02/17/2014] [Indexed: 12/16/2022]
Abstract
DESCRIPTIONS The structure of a GH19 chitinase from the moss Bryum coronatum (BcChi-A) in complex with the substrate was examined by X-ray crystallography and NMR spectroscopy in solution. The X-ray crystal structure of the inactive mutant of BcChi-A (BcChi-A-E61A) liganded with chitin tetramer (GlcNAc)4 revealed a clear electron density of the tetramer bound to subsites -2, -1, +1, and +2. Individual sugar residues were recognized by several amino acids at these subsites through a number of hydrogen bonds. This is the first crystal structure of GH19 chitinase liganded with oligosaccharide spanning the catalytic center. NMR titration experiments of chitin oligosaccharides into the BcChi-A-E61A solution showed that the binding mode observed in the crystal structure is similar to that in solution. The C-1 carbon of -1 GlcNAc, the Oε1 atom of the catalytic base (Glu70), and the Oγ atom of Ser102 form a "triangle" surrounding the catalytic water, and the arrangement structurally validated the proposed catalytic mechanism of GH19 chitinases. The glycosidic linkage between -1 and +1 sugars was found to be twisted and under strain. This situation may contribute to the reduction of activation energy for hydrolysis. The complex structure revealed a more refined mechanism of the chitinase catalysis.
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Mayes HB, Broadbelt LJ, Beckham GT. How Sugars Pucker: Electronic Structure Calculations Map the Kinetic Landscape of Five Biologically Paramount Monosaccharides and Their Implications for Enzymatic Catalysis. J Am Chem Soc 2014; 136:1008-22. [DOI: 10.1021/ja410264d] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- National
Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Linda J. Broadbelt
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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Cuyvers S, Dornez E, Delcour JA, Courtin CM. Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 2011; 32:93-107. [DOI: 10.3109/07388551.2011.561537] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyémánt G, Næsted H, Kandra L, Sigurskjold BW, Svensson B. Two Secondary Carbohydrate Binding Sites on the Surface of Barley α-Amylase 1 Have Distinct Functions and Display Synergy in Hydrolysis of Starch Granules. Biochemistry 2009; 48:7686-97. [DOI: 10.1021/bi900795a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Morten M. Nielsen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Sophie Bozonnet
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
| | - Eun-Seong Seo
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - János A. Mótyán
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Joakim M. Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Gyöngyi Gyémánt
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Henrik Næsted
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Lili Kandra
- Department of Biochemistry, Faculty of Sciences, University of Debrecen, Debrecen, Hungary H-4010
| | - Bent W. Sigurskjold
- Department of Biology, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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Karaveg K, Siriwardena A, Tempel W, Liu ZJ, Glushka J, Wang BC, Moremen KW. Mechanism of Class 1 (Glycosylhydrolase Family 47) α-Mannosidases Involved in N-Glycan Processing and Endoplasmic Reticulum Quality Control. J Biol Chem 2005; 280:16197-207. [PMID: 15713668 DOI: 10.1074/jbc.m500119200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quality control in the endoplasmic reticulum (ER) determines the fate of newly synthesized glycoproteins toward either correct folding or disposal by ER-associated degradation. Initiation of the disposal process involves selective trimming of N-glycans attached to misfolded glycoproteins by ER alpha-mannosidase I and subsequent recognition by the ER degradation-enhancing alpha-mannosidase-like protein family of lectins, both members of glycosylhydrolase family 47. The unusual inverting hydrolytic mechanism catalyzed by members of this family is investigated here by a combination of kinetic and binding analyses of wild type and mutant forms of human ER alpha-mannosidase I as well as by structural analysis of a co-complex with an uncleaved thiodisaccharide substrate analog. These data reveal the roles of potential catalytic acid and base residues and the identification of a novel (3)S(1) sugar conformation for the bound substrate analog. The co-crystal structure described here, in combination with the (1)C(4) conformation of a previously identified co-complex with the glycone mimic, 1-deoxymannojirimycin, indicates that glycoside bond cleavage proceeds through a least motion conformational twist of a properly predisposed substrate in the -1 subsite. A novel (3)H(4) conformation is proposed as the exploded transition state.
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Affiliation(s)
- Khanita Karaveg
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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Kang YN, Adachi M, Utsumi S, Mikami B. The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase. J Mol Biol 2004; 339:1129-40. [PMID: 15178253 DOI: 10.1016/j.jmb.2004.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Revised: 04/07/2004] [Accepted: 04/08/2004] [Indexed: 11/18/2022]
Abstract
It has previously been suggested that the glutamic acid residues Glu186 and Glu380 of soybean beta-amylase play critical roles as a general acid and a general base catalyst, respectively. In order to confirm the roles of Glu186 and Glu380, each residue was mutated to a glutamine residue and the crystal structures of the substrate (E186Q/maltopentaose) and product (E380Q/maltose) complexes were determined at resolutions of 1.6 Angstrom and 1.9 Angstrom, respectively. Both mutant enzymes exhibited 16,000- and 37,000-fold decreased activity relative to that of the wild-type enzyme. The crystal structure of the E186Q/maltopentaose complex revealed an unambiguous five-glucose unit at subsites -2 to +3. Two maltose molecules bind on subsites -2 to -1 and +2 to +3 in the E380Q/maltose complex, whereas they bind in tandem to -2 to -1 and +1 to +2 in the wild-type/maltose complex. The conformation of the glucose residue at subsite -1 was identified as a stable (4)C(1) alpha-anomer in the E380Q/maltose complex, whereas a distorted ring conformation was observed in the wild-type/maltose complex. The side-chain movement of Gln380 to the position of a putative attacking water molecule seen in the wild-type enzyme caused the inactivation of the E380Q mutant and an altered binding pattern of maltose molecules. These results confirm the critical roles played by Glu186 in the donation of a proton to the glycosidic oxygen of the substrate, and by Glu380 in the activation of an attacking water molecule. The observed difference between the backbones of E186Q/maltopentaose and E380Q/maltose in terms of Thr342 suggests that the side-chain of Thr342 may stabilize the deprotonated form of Glu186 after the cleavage of the glycosidic bond.
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Affiliation(s)
- You-Na Kang
- Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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