1
|
Glasgow EM, Kemna EI, Bingman CA, Ing N, Deng K, Bianchetti CM, Takasuka TE, Northen TR, Fox BG. A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. J Biol Chem 2021; 295:17752-17769. [PMID: 33454012 DOI: 10.1074/jbc.ra120.015328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/15/2020] [Indexed: 11/06/2022] Open
Abstract
Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)-linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.
Collapse
Affiliation(s)
- Evan M Glasgow
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Elias I Kemna
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Nicole Ing
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Christopher M Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | | | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, California, USA; Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA.
| |
Collapse
|
2
|
Wang W, Archbold T, Lam JS, Kimber MS, Fan MZ. A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota. Sci Rep 2019; 9:13630. [PMID: 31541154 PMCID: PMC6754456 DOI: 10.1038/s41598-019-50050-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/05/2019] [Indexed: 02/08/2023] Open
Abstract
Cellulases play important roles in the dietary fibre digestion in pigs, and have multiple industrial applications. The porcine intestinal microbiota display a unique feature in rapid cellulose digestion. Herein, we have expressed a cellulase gene, p4818Cel5_2A, which singly encoded a catalytic domain belonging to glycoside hydrolase family 5 subfamily 2, and was previously identified from a metagenomic expression library constructed from porcine gut microbiome after feeding grower pigs with a cellulose-supplemented diet. The activity of purified p4818Cel5_2A was maximal at pH 6.0 and 50 °C and displayed resistance to trypsin digestion. This enzyme exhibited activities towards a wide variety of plant polysaccharides, including cellulosic substrates of avicel and solka-Floc®, and the hemicelluloses of β-(1 → 4)/(1 → 3)-glucans, xyloglucan, glucomannan and galactomannan. Viscosity, reducing sugar distribution and hydrolysis product analyses further revealed that this enzyme was a processive endo-β-(1 → 4)-glucanase capable of hydrolyzing cellulose into cellobiose and cellotriose as the primary end products. These catalytic features of p4818Cel5_2A were further explored in the context of a three-dimensional homology model. Altogether, results of this study report a microbial processive endoglucanase identified from the porcine gut microbiome, and it may be tailored as an efficient biocatalyst candidate for potential industrial applications.
Collapse
Affiliation(s)
- Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Tania Archbold
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Joseph S Lam
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Matthew S Kimber
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ming Z Fan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| |
Collapse
|
3
|
A building block approach to the synthesis of a family of S-linked α-1,6-oligomannosides. Carbohydr Res 2016; 429:38-47. [DOI: 10.1016/j.carres.2016.04.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022]
|
4
|
Lázár L, Csávás M, Herczeg M, Herczegh P, Borbás A. Synthesis of S-Linked Glycoconjugates and S-Disaccharides by Thiol–Ene Coupling Reaction of Enoses. Org Lett 2012; 14:4650-3. [DOI: 10.1021/ol302098u] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- László Lázár
- Research Group for Carbohydrates, University of Debrecen, P.O. Box 94, H-4010 Debrecen, Hungary, and Department of Pharmaceutical Chemistry, Medical and Health Science Center, University of Debrecen, P.O. Box 70, H-4010 Debrecen, Hungary
| | - Magdolna Csávás
- Research Group for Carbohydrates, University of Debrecen, P.O. Box 94, H-4010 Debrecen, Hungary, and Department of Pharmaceutical Chemistry, Medical and Health Science Center, University of Debrecen, P.O. Box 70, H-4010 Debrecen, Hungary
| | - Mihály Herczeg
- Research Group for Carbohydrates, University of Debrecen, P.O. Box 94, H-4010 Debrecen, Hungary, and Department of Pharmaceutical Chemistry, Medical and Health Science Center, University of Debrecen, P.O. Box 70, H-4010 Debrecen, Hungary
| | - Pál Herczegh
- Research Group for Carbohydrates, University of Debrecen, P.O. Box 94, H-4010 Debrecen, Hungary, and Department of Pharmaceutical Chemistry, Medical and Health Science Center, University of Debrecen, P.O. Box 70, H-4010 Debrecen, Hungary
| | - Anikó Borbás
- Research Group for Carbohydrates, University of Debrecen, P.O. Box 94, H-4010 Debrecen, Hungary, and Department of Pharmaceutical Chemistry, Medical and Health Science Center, University of Debrecen, P.O. Box 70, H-4010 Debrecen, Hungary
| |
Collapse
|
5
|
Gandhi NS, Freeman C, Parish CR, Mancera RL. Computational analyses of the catalytic and heparin-binding sites and their interactions with glycosaminoglycans in glycoside hydrolase family 79 endo-β-d-glucuronidase (heparanase). Glycobiology 2011; 22:35-55. [DOI: 10.1093/glycob/cwr095] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
6
|
Sukharnikov LO, Cantwell BJ, Podar M, Zhulin IB. Cellulases: ambiguous nonhomologous enzymes in a genomic perspective. Trends Biotechnol 2011; 29:473-9. [PMID: 21683463 DOI: 10.1016/j.tibtech.2011.04.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 01/30/2023]
Abstract
The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most of the biochemically characterized bacterial cellulases come from only a few cellulose-degrading bacteria, thus limiting our knowledge of a range of cellulolytic activities that exist in nature. The recent explosion of genomic data offers a unique opportunity to search for novel cellulolytic activities; however, the absence of clear understanding of structural and functional features that are important for reliable computational identification of cellulases precludes their exploration in the genomic datasets. Here, we explore the diversity of cellulases and propose a genomic approach to overcome this bottleneck.
Collapse
Affiliation(s)
- Leonid O Sukharnikov
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | | | |
Collapse
|
7
|
A β‐1,4‐Galactosyltransferase fromHelicobacter pyloriis an Efficient and Versatile Biocatalyst Displaying a Novel Activity for Thioglycoside Synthesis. Chembiochem 2008; 9:1632-40. [DOI: 10.1002/cbic.200700775] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
8
|
Kim YW, Chen HM, Kim JH, Müllegger J, Mahuran D, Withers SG. Thioglycoligase-based assembly of thiodisaccharides: screening as beta-galactosidase inhibitors. Chembiochem 2007; 8:1495-9. [PMID: 17661304 PMCID: PMC2910745 DOI: 10.1002/cbic.200700263] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Young-Wan Kim
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | | | | | | | | |
Collapse
|
9
|
Buser S, Vasella A. Synthesis of 2-Azabicyclo[3.2.2]nonane-Derived Monosaccharide Mimics and Their Evaluation as Glycosidase Inhibitors. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
10
|
Buser S, Vasella A. 7-Oxanorbornane and Norbornane Mimics of a Distortedβ-D-Mannopyranoside: Synthesis and Evaluation asβ-Mannosidase Inhibitors. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590255] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
11
|
Sandgren M, Berglund GI, Shaw A, Ståhlberg J, Kenne L, Desmet T, Mitchinson C. Crystal Complex Structures Reveal How Substrate is Bound in the −4 to the +2 Binding Sites of Humicola grisea Cel12A. J Mol Biol 2004; 342:1505-17. [PMID: 15364577 DOI: 10.1016/j.jmb.2004.07.098] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Revised: 07/19/2004] [Accepted: 07/30/2004] [Indexed: 11/27/2022]
Abstract
As part of an ongoing enzyme discovery program to investigate the properties and catalytic mechanism of glycoside hydrolase family 12 (GH 12) endoglucanases, a GH family that contains several cellulases that are of interest in industrial applications, we have solved four new crystal structures of wild-type Humicola grisea Cel12A in complexes formed by soaking with cellobiose, cellotetraose, cellopentaose, and a thio-linked cellotetraose derivative (G2SG2). These complex structures allow mapping of the non-covalent interactions between the enzyme and the glucosyl chain bound in subsites -4 to +2 of the enzyme, and shed light on the mechanism and function of GH 12 cellulases. The unhydrolysed cellopentaose and the G2SG2 cello-oligomers span the active site of the catalytically active H.grisea Cel12A enzyme, with the pyranoside bound in subsite -1 displaying a S31 skew boat conformation. After soaking in cellotetraose, the cello-oligomer that is found bound in site -4 to -1 contains a beta-1,3-linkage between the two cellobiose units in the oligomer, which is believed to have been formed by a transglycosylation reaction that has occurred during the ligand soak of the protein crystals. The close fit of this ligand and the binding sites occupied suggest a novel mixed beta-glucanase activity for this enzyme.
Collapse
Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
| | | | | | | | | | | | | |
Collapse
|
12
|
Hrmova M, De Gori R, Smith BJ, Vasella A, Varghese JN, Fincher GB. Three-dimensional Structure of the Barley β-d-Glucan Glucohydrolase in Complex with a Transition State Mimic. J Biol Chem 2004; 279:4970-80. [PMID: 14597633 DOI: 10.1074/jbc.m307188200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucophenylimidazole (PheGlcIm), a tetrahydroimidazopyridine-type inhibitor and 4H3 conformer mimic of a glucoside, binds very tightly to a barley beta-d-glucan glucohydrolase, with a Ki constant of 2 x 10(-9) m and a DeltaG of 51 kJ mol(-1). PheGlcIm binds to the barley beta-d-glucan glucohydrolase approximately 2 x 10(5) times tighter than laminarin, which is the best non-synthetic ground-state substrate found so far for this enzyme, 10(6) times tighter than 4-nitrophenyl beta-d-glucopyranoside, and 2 x 10(7) tighter than glucose. The three-dimensional structure of the beta-d-glucan glucohydrolase with bound PheGlcIm indicates that the complex resembles a hypothetical transition state during the hydrolytic cycle, that the enzyme derives substrate binding energy from the "aglycone" portion of the ligand, and that it also reveals an anti-protonation trajectory for hydrolysis. Continuous electron densities at the 1.6 sigma level form between the three active site residues Asp95, His207, and Asp285, and the C6OH, C7OH, C8OH, and C9OH groups of PheGlcIm. These electron densities correspond to the most favorable interactions in the three-dimensional structure of the beta-d-glucan glucohydrolase-PheGlcIm complex and indicate atomic distances equal to or less than 2.55 A. The crystallographic data were corroborated with ab initio molecular orbital calculations. The data indicate that the 4E conformation of the glucose part of PheGlcIm is critical for tight binding and provide the first evidence for probable substrate distortion during catalysis by this enzyme.
Collapse
Affiliation(s)
- Maria Hrmova
- Faculty of Sciences, School of Agriculture and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
| | | | | | | | | | | |
Collapse
|
13
|
Abstract
The three-dimensional structure of glycosidases and of their complexes and the study of transition-state mimics reveal structural details that correlate with mechanism. Of particular interest are the transition-state conformations harnessed by individual enzymes and the substrate distortion observed in enzyme-ligand complexes. 3D-structure in synergy with transition-state mimicry opens the way for mechanistic interpretation of enzyme inhibition and for the development of therapeutic agents.
Collapse
Affiliation(s)
- Andrea Vasella
- Laboratorium für Organische Chemie, ETH Hönggerberg, HCI H317, CH-8093 Zürich, Switzerland
| | | | | |
Collapse
|
14
|
Lo Leggio L, Larsen S. The 1.62 A structure of Thermoascus aurantiacus endoglucanase: completing the structural picture of subfamilies in glycoside hydrolase family 5. FEBS Lett 2002; 523:103-8. [PMID: 12123813 DOI: 10.1016/s0014-5793(02)02954-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The crystal structure of Thermoascus aurantiacus endoglucanase (Cel5A), a family 5 glycoside hydrolase, has been determined to 1.62 A resolution by multiple isomorphous replacement with anomalous scattering. It is the first report of a structure in the subfamily to which Cel5A belongs. Cel5A consists solely of a catalytic module with compact eight-fold beta/alpha barrel architecture. The length of the tryptophan-rich substrate binding groove suggests the presence of substrate binding subsites -4 to +3. Structural comparison shows that two glycines are completely conserved in the family, in addition to the two catalytic glutamates and six other conserved residues previously identified. Gly 44 in particular is part of a type IV C-terminal helix capping motif, whose disruption is likely to affect the position of an essential conserved arginine. One aromatic residue (Trp 170 in Cel5A), not conserved in term of sequence, is nonetheless spatially conserved in the substrate binding groove. Its role might be to force the bend that occurs in the polysaccharide chain on binding, thus favoring substrate distortion at subsite -1.
Collapse
Affiliation(s)
- Leila Lo Leggio
- Centre for Crystallographic Studies, Department of Chemistry, Chemical Institute, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark.
| | | |
Collapse
|
15
|
Abstract
Oligosaccharides in which at least one glycosidic oxygen atom is replaced with a sulfur atom can be routinely synthesized and act as competitive inhibitors of various glycoside hydrolases. Recent studies using both X-ray crystallography and other biophysical techniques provide structural insight into binding, recognition, and the catalytic mechanism of action of these enzymes.
Collapse
Affiliation(s)
- H Driguez
- Centre de Recherches sur les Macromolécules Végétales (CERMAV-CNRS), Affiliated with Université Joseph Fourier, Grenoble B.P. 53, 38041 Grenoble cedex 9, France.
| |
Collapse
|