1
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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2
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Lipsh-Sokolik R, Khersonsky O, Schröder SP, de Boer C, Hoch SY, Davies GJ, Overkleeft HS, Fleishman SJ. Combinatorial assembly and design of enzymes. Science 2023; 379:195-201. [PMID: 36634164 DOI: 10.1126/science.ade9434] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.
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Affiliation(s)
- R Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - O Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S P Schröder
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - C de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S-Y Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - G J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
| | - H S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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3
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Mazurkewich S, Poulsen JCN, Lo Leggio L, Larsbrink J. Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components. J Biol Chem 2019; 294:19978-19987. [PMID: 31740581 PMCID: PMC6937553 DOI: 10.1074/jbc.ra119.011435] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Indexed: 12/28/2022] Open
Abstract
Glucuronoyl esterases (GEs) catalyze the cleavage of ester linkages between lignin and glucuronic acid moieties on glucuronoxylan in plant biomass. As such, GEs represent promising biochemical tools in industrial processing of these recalcitrant resources. However, details on how GEs interact and catalyze degradation of their natural substrates are sparse, calling for thorough enzyme structure-function studies. Presented here is a structural and mechanistic investigation of the bacterial GE OtCE15A. GEs belong to the carbohydrate esterase family 15 (CE15), which is in turn part of the larger α/β-hydrolase superfamily. GEs contain a Ser-His-Asp/Glu catalytic triad, but the location of the catalytic acid in GEs has been shown to be variable, and OtCE15A possesses two putative catalytic acidic residues in the active site. Through site-directed mutagenesis, we demonstrate that these residues are functionally redundant, possibly indicating the evolutionary route toward new functionalities within the family. Structures determined with glucuronate, in both native and covalently bound intermediate states, and galacturonate provide insights into the catalytic mechanism of CE15. A structure of OtCE15A with the glucuronoxylooligosaccharide 23-(4-O-methyl-α-d-glucuronyl)-xylotriose (commonly referred to as XUX) shows that the enzyme can indeed interact with polysaccharides from the plant cell wall, and an additional structure with the disaccharide xylobiose revealed a surface binding site that could possibly indicate a recognition mechanism for long glucuronoxylan chains. Collectively, the results indicate that OtCE15A, and likely most of the CE15 family, can utilize esters of glucuronoxylooligosaccharides and support the proposal that these enzymes work on lignin-carbohydrate complexes in plant biomass.
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Affiliation(s)
- Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | | | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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4
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Sunden F, AlSadhan I, Lyubimov A, Doukov T, Swan J, Herschlag D. Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution. J Biol Chem 2017; 292:20960-20974. [PMID: 29070681 DOI: 10.1074/jbc.m117.788240] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/19/2017] [Indexed: 11/06/2022] Open
Abstract
Members of enzyme superfamilies specialize in different reactions but often exhibit catalytic promiscuity for one another's reactions, consistent with catalytic promiscuity as an important driver in the evolution of new enzymes. Wanting to understand how catalytic promiscuity and other factors may influence evolution across a superfamily, we turned to the well-studied alkaline phosphatase (AP) superfamily, comparing three of its members, two evolutionarily distinct phosphatases and a phosphodiesterase. We mutated distinguishing active-site residues to generate enzymes that had a common Zn2+ bimetallo core but little sequence similarity and different auxiliary domains. We then tested the catalytic capabilities of these pruned enzymes with a series of substrates. A substantial rate enhancement of ∼1011-fold for both phosphate mono- and diester hydrolysis by each enzyme indicated that the Zn2+ bimetallo core is an effective mono/di-esterase generalist and that the bimetallo cores were not evolutionarily tuned to prefer their cognate reactions. In contrast, our pruned enzymes were ineffective sulfatases, and this limited promiscuity may have provided a driving force for founding the distinct one-metal-ion branch that contains all known AP superfamily sulfatases. Finally, our pruned enzymes exhibited 107-108-fold phosphotriesterase rate enhancements, despite absence of such enzymes within the AP superfamily. We speculate that the superfamily active-site architecture involved in nucleophile positioning prevents accommodation of the additional triester substituent. Overall, we suggest that catalytic promiscuity, and the ease or difficulty of remodeling and building onto existing protein scaffolds, have greatly influenced the course of enzyme evolution. Uncovering principles and properties of enzyme function, promiscuity, and repurposing provides lessons for engineering new enzymes.
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Affiliation(s)
- Fanny Sunden
- From the Department of Biochemistry, Beckman Center
| | | | - Artem Lyubimov
- the Departments of Molecular and Cellular Physiology.,Neurology and Neurological Science.,Structural Biology, and.,Photon Science.,Howard Hughes Medical Institute
| | - Tzanko Doukov
- the Macromolecular Crystallographic Group, Stanford Synchrotron Radiation Lightsource, National Accelerator Laboratory, Stanford University, Stanford, California 94309
| | - Jeffrey Swan
- From the Department of Biochemistry, Beckman Center
| | - Daniel Herschlag
- From the Department of Biochemistry, Beckman Center, .,the Departments of Chemical Engineering and Chemistry, and.,Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305 and
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5
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Fan XJ, Yang C, Zhang C, Ren H, Zhang JD. Cloning, Site-Directed Mutagenesis, and Functional Analysis of Active Residues in Lymantria dispar Chitinase. Appl Biochem Biotechnol 2017; 184:12-24. [PMID: 28577192 DOI: 10.1007/s12010-017-2524-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Chitinases are glycosyl hydrolases that catalyze the hydrolysis of β-(1,4)-glycosidic bonds in chitin, the major structural polysaccharide presented in the cuticle and gut peritrophic matrix of insects. Two aspartate residues (D143, D145) and one tryptophan (W146) in the Lymantria dispar chitinase are highly conserved residues observed within the second conserved motif of the family 18 chitinase catalytic region. In this study, a chitinase cDNA, LdCht5, was cloned from L. dispar, and the roles of the three residues were investigated using site-directed mutagenesis and substituting them with three other amino acids. Seven mutant proteins, D143E, D145E, W146G, D143E/D145E, D143E/W146G, D145E/W146G, and D143E/D145E/W146G, as well as the wild-type enzyme, were produced using the baculovirus-insect cell line expression system. The enzymatic and kinetic properties of these mutant enzymes were measured using the oligosaccharide substrate MU-(GlcNAc)3. Among the seven mutants, the D145E, D143E/D145E, and D145E/W146G mutations kept some extant catalytic activity toward MU-(GlcNAc)3, while the D143E, W146G, D143E/W146G, and D143E/D145E/W146G mutant enzymes were inactivated. Compared with the mutant enzymes, the wild-type enzyme had higher values of k cat and k cat / K m . A study of the multiple point mutations in the second conserved catalytic region would help to elucidate the role of the critical residues and their relationships.
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Affiliation(s)
- Xiao-Jun Fan
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No. 79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Chun Yang
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No. 79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Chang Zhang
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No. 79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Hui Ren
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No. 79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Jian-Dong Zhang
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No. 79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China.
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6
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Bissaro B, Durand J, Biarnés X, Planas A, Monsan P, O’Donohue MJ, Fauré R. Molecular Design of Non-Leloir Furanose-Transferring Enzymes from an α-l-Arabinofuranosidase: A Rationale for the Engineering of Evolved Transglycosylases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00949] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bastien Bissaro
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Julien Durand
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Xevi Biarnés
- Laboratory
of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory
of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 08017 Barcelona, Spain
| | - Pierre Monsan
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- Toulouse White
Biotechnology, UMS INRA/INSA 1337, UMS CNRS/INSA 3582, 3 Rue des Satellites, 31400 Toulouse, France
| | - Michael J. O’Donohue
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
| | - Régis Fauré
- Université
de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792,
Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
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7
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Duo T, Goddard-Borger ED, Withers SG. Fluoro-glycosyl acridinones are ultra-sensitive active site titrating agents for retaining β-glycosidases. Chem Commun (Camb) 2015; 50:9379-82. [PMID: 25004867 DOI: 10.1039/c4cc03299c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Novel fluorogenic 2-deoxy-2-fluoroglycosyl acridinone active site titrating reagents were synthesised and kinetic parameters determined for their inactivation of two retaining β-glucosidases, a β-galactosidase, a β-xylosidase and several cellulases. Fluorescence-monitored active site titration using this class of reagents reliably measured active enzyme concentrations down to 3 nM.
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Affiliation(s)
- Tianmeng Duo
- The Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1.
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8
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Xie M, Byers LD. Solvent and α-secondary kinetic isotope effects on β-glucosidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1776-81. [PMID: 25770682 DOI: 10.1016/j.bbapap.2015.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/23/2015] [Indexed: 11/20/2022]
Abstract
β-Glucosidase from sweet almond is a retaining, family 1, glycohydrolase. It is known that glycosylation of the enzyme by aryl glucosides occurs with little, if any, acid catalysis. For this reaction both the solvent and α-secondary kinetic isotope effects are 1.0. However, for the deglucosylation reaction (e.g., kcat for 2,4-dinitrophenyl-β-D-glucopyranoside) there is a small solvent deuterium isotope effect of 1.50 (±0.06) and an α-secondary kinetic isotope effect of 1.12 (±0.03). For aryl glucosides, kcat/KM is very sensitive to the pKa of the phenol leaving group [βlg≈-1; Dale et al., Biochemistry25 (1986) 2522-2529]. With alkyl glucosides the βlg is smaller (between -0.2 and -0.3) but still negative. This, coupled with the small solvent isotope effect on the pH-independent second-order rate constant for the glucosylation of the enzyme with 2,2,2-trifluoroethyl-β-glucoside [D2O(kcat/KM)=1.23 (±0.04)] suggests that there is more glycone-aglycone bond fission than aglycone oxygen protonation in the transition state for alkyl glycoside hydrolysis. The kinetics constants for the partitioning (between water and various alcohols) of the glucosyl-enzyme intermediate, coupled with the rate constants for the forward (hydrolysis) reaction provide an estimate of the stability of the glucosyl-enzyme intermediate. This is a relatively stable species with an energy about 2 to 4 kcal/mol higher than that of the ES complex. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Miaomiao Xie
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Larry D Byers
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
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9
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McCleary BV, Mangan D, Daly R, Fort S, Ivory R, McCormack N. Novel substrates for the measurement of endo-1,4-β-glucanase (endo-cellulase). Carbohydr Res 2014; 385:9-17. [DOI: 10.1016/j.carres.2013.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/02/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
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10
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Jongkees SAK, Yoo H, Withers SG. Mechanistic Insights from Substrate Preference in Unsaturated Glucuronyl Hydrolase. Chembiochem 2013; 15:124-34. [PMID: 24227702 DOI: 10.1002/cbic.201300547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Seino A K Jongkees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1 (Canada)
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11
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Sikowitz MD, Cooper L, Begley TP, Kaminski PA, Ealick SE. Reversal of the substrate specificity of CMP N-glycosidase to dCMP. Biochemistry 2013; 52:4037-47. [PMID: 23659472 PMCID: PMC3750073 DOI: 10.1021/bi400316p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
MilB is a CMP hydrolase involved in the early steps of biosynthesis of the antifungal compound mildiomycin. An enzyme from the bacimethrin biosynthetic pathway, BcmB, is closely related to MilB in both sequence and function. These two enzymes belong to the nucleoside 2'-deoxyribosyltransferase (NDT) superfamily. NDTs catalyze N-glycosidic bond cleavage of 2'-deoxynucleosides via a covalent 2-deoxyribosyl-enzyme intermediate. Conservation of key active site residues suggests that members of the NDT superfamily share a common mechanism; however, the enzymes differ in their substrate preferences. Substrates vary in the type of nucleobase, the presence or absence of a 2'-hydroxyl group, and the presence or absence of a 5'-phosphate group. We have determined the structures of MilB and BcmB and compared them to previously determined structures of NDT superfamily members. The comparisons reveal how these enzymes differentiate between ribosyl and deoxyribosyl nucleotides or nucleosides and among different nucleobases. The 1.6 Å structure of the MilB-CMP complex reveals an active site feature that is not obvious from comparisons of sequence alone. MilB and BcmB that prefer substrates containing 2'-ribosyl groups have a phenylalanine positioned in the active site, whereas NDT family members with a preference for 2'-deoxyribosyl groups have a tyrosine residue. Further studies show that the phenylalanine is critical for the specificity of MilB and BcmB toward CMP, and mutation of this phenylalanine residue to tyrosine results in a 1000-fold reversal of substrate specificity from CMP to dCMP.
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Affiliation(s)
- Megan D. Sikowitz
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Lisa Cooper
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | | | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227.
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12
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Development of inhibitors as research tools for carbohydrate-processing enzymes. Biochem Soc Trans 2012; 40:913-28. [DOI: 10.1042/bst20120201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates, which are present in all domains of life, play important roles in a host of cellular processes. These ubiquitous biomolecules form highly diverse and often complex glycan structures without the aid of a template. The carbohydrate structures are regulated solely by the location and specificity of the enzymes responsible for their synthesis and degradation. These enzymes, glycosyltransferases and glycoside hydrolases, need to be functionally well characterized in order to investigate the structure and function of glycans. The use of enzyme inhibitors, which target a particular enzyme, can significantly aid this understanding, and may also provide insights into therapeutic applications. The present article describes some of the approaches used to design and develop enzyme inhibitors as tools for investigating carbohydrate-processing enzymes.
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13
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QM/MM study of catalytic mechanism of Xylanase Cex from Cellulomonas fimi. J Mol Graph Model 2012; 37:67-76. [DOI: 10.1016/j.jmgm.2012.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/01/2012] [Accepted: 04/17/2012] [Indexed: 12/13/2022]
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14
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Cruys-Bagger N, Elmerdahl J, Praestgaard E, Tatsumi H, Spodsberg N, Borch K, Westh P. Pre-steady-state kinetics for hydrolysis of insoluble cellulose by cellobiohydrolase Cel7A. J Biol Chem 2012; 287:18451-8. [PMID: 22493488 DOI: 10.1074/jbc.m111.334946] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transient kinetic behavior of enzyme reactions prior to the establishment of steady state is a major source of mechanistic information, yet this approach has not been utilized for cellulases acting on their natural substrate, insoluble cellulose. Here, we elucidate the pre-steady-state regime for the exo-acting cellulase Cel7A using amperometric biosensors and an explicit model for processive hydrolysis of cellulose. This analysis allows the identification of a pseudo-steady-state period and quantification of a processivity number as well as rate constants for the formation of a threaded enzyme complex, processive hydrolysis, and dissociation, respectively. These kinetic parameters elucidate limiting factors in the cellulolytic process. We concluded, for example, that Cel7A cleaves about four glycosidic bonds/s during processive hydrolysis. However, the results suggest that stalling the processive movement and low off-rates result in a specific activity at pseudo-steady state that is 10-25-fold lower. It follows that the dissociation of the enzyme-substrate complex (half-time of ~30 s) is rate-limiting for the investigated system. We suggest that this approach can be useful in attempts to unveil fundamental reasons for the distinctive variability in hydrolytic activity found in different cellulase-substrate systems.
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Affiliation(s)
- Nicolaj Cruys-Bagger
- Department of Science, Systems, and Models, Roskilde University, Roskilde, Denmark
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15
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Goddard-Borger ED, Sakaguchi K, Reitinger S, Watanabe N, Ito M, Withers SG. Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass. J Am Chem Soc 2012; 134:3895-902. [PMID: 22296113 DOI: 10.1021/ja211836t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xylanases capable of degrading the crystalline microfibrils of 1,3-xylan that reinforce the cell walls of some red and siphonous green algae have not been well studied, yet they could prove to be of great utility in algaculture for the production of food and renewable chemical feedstocks. To gain a better mechanistic understanding of these enzymes, a suite of reagents was synthesized and evaluated as substrates and inhibitors of an endo-1,3-xylanase. With these reagents, a retaining mechanism was confirmed for the xylanase, its catalytic nucleophile identified, and the existence of -3 to +2 substrate-binding subsites demonstrated. Protein crystal X-ray diffraction methods provided a high resolution structure of a trapped covalent glycosyl-enzyme intermediate, indicating that the 1,3-xylanases likely utilize the (1)S(3) → (4)H(3) → (4)C(1) conformational itinerary to effect catalysis.
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Affiliation(s)
- Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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16
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Yang H, Wang K, Song X, Xu F. Production of xylooligosaccharides by xylanase from Pichia stipitis based on xylan preparation from triploid Populas tomentosa. BIORESOURCE TECHNOLOGY 2011; 102:7171-7176. [PMID: 21565493 DOI: 10.1016/j.biortech.2011.03.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 05/30/2023]
Abstract
Xylooligosaccharides (XOS) with DP 2-4 are important synbiotics used as food ingredients based on its prebiotic characteristics. In this work, the production of XOS from lignocellulosic material was performed by combined chemical-enzymatic methods. Xylan was prepared from triploid Populas tomentosa, and bioconverted into XOS by crude xylanase solution obtained from Pichia stipitis. The effects of reaction time, temperature, enzyme dosage, and pH value on the production of XOS were fully evaluated. Under the optimal condition (25U g(-1) substrate, pH 5.4 and 50°C), 36.8% of the xylan preparation was converted to XOS, equivalent to 3.95 mg/mL of the hydrolyzate. Xylobiose, xylotriose and xylotetrose were analyzed to be the main products of the enzymatic hydrolyzate, which together accounted for over 95% of the released oligosaccharides. Meanwhile, the effect of sonication pretreatment on the conversion efficiency of the xylan preparation was also investigated.
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Affiliation(s)
- Haiyan Yang
- Institute of Biomass Chemistry and Technology, College of Material Science and Technology, Beijing Forestry University, Beijing, 100083, China
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17
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Mewis K, Taupp M, Hallam SJ. A high throughput screen for biomining cellulase activity from metagenomic libraries. J Vis Exp 2011:2461. [PMID: 21307835 DOI: 10.3791/2461] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cellulose, the most abundant source of organic carbon on the planet, has wide-ranging industrial applications with increasing emphasis on biofuel production (1). Chemical methods to modify or degrade cellulose typically require strong acids and high temperatures. As such, enzymatic methods have become prominent in the bioconversion process. While the identification of active cellulases from bacterial and fungal isolates has been somewhat effective, the vast majority of microbes in nature resist laboratory cultivation. Environmental genomic, also known as metagenomic, screening approaches have great promise in bridging the cultivation gap in the search for novel bioconversion enzymes. Metagenomic screening approaches have successfully recovered novel cellulases from environments as varied as soils (2), buffalo rumen (3) and the termite hind-gut (4) using carboxymethylcellulose (CMC) agar plates stained with congo red dye (based on the method of Teather and Wood (5)). However, the CMC method is limited in throughput, is not quantitative and manifests a low signal to noise ratio (6). Other methods have been reported (7,8) but each use an agar plate-based assay, which is undesirable for high-throughput screening of large insert genomic libraries. Here we present a solution-based screen for cellulase activity using a chromogenic dinitrophenol (DNP)-cellobioside substrate (9). Our library was cloned into the pCC1 copy control fosmid to increase assay sensitivity through copy number induction (10). The method uses one-pot chemistry in 384-well microplates with the final readout provided as an absorbance measurement. This readout is quantitative, sensitive and automated with a throughput of up to 100X 384-well plates per day using a liquid handler and plate reader with attached stacking system.
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Affiliation(s)
- Keith Mewis
- Microbiology and Immunology, University of British Columbia - UBC
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18
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Nishimoto M, Kobayashi A, Honda Y, Kitaoka M, Hayashi K. p-Nitrophenyl β-Glycosides of β-1,4-Gluco/xylo-disaccharides for the Characterization of Subsites in Endo-xylanases. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2010_024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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19
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Planas A, Nieto J, Abel M, Segade A. Unusual Role of the 3-OH Group of Oligosaccharide Substrates in the Mechanism ofBacillus1,3-1,4-β-glucanase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001618500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Willis LM, Zhang R, Reid A, Withers SG, Wakarchuk WW. Mechanistic investigation of the endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae R6. Biochemistry 2009; 48:10334-41. [PMID: 19788271 DOI: 10.1021/bi9013825] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large (1767-amino acid) endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae (SpGH101) specifically removes an O-linked disaccharide Gal-beta-1,3-GalNAc-alpha from glycoproteins. While the enzyme from natural sources has been used as a reagent for many years, very few mechanistic studies have been performed. Using the recently determined three-dimensional structure of the recombinant protein as a background, we report here a mechanistic investigation of the SpGH101 retaining alpha-glycoside hydrolase using a combination of synthetic and natural substrates. On the basis of a model of the substrate complex of SpGH101, we propose D764 and E796 as the nucleophile and general acid-base residues, respectively. These roles were confirmed by kinetic and mechanistic analysis of mutants at those positions using synthetic substrates and anion rescue experiments. pK(a) values of 5.3 and 7.2 were assigned to D764 and E796 on the basis of the pK(a) values derived from the bell-shaped dependence of k(cat)/K(m) upon pH. The enzyme contains several putative carbohydrate binding modules whose glycan binding specificities were probed using the printed glycan array of the Consortium for Functional Glycomics using the inactive D764A and D764F mutants that had been labeled with Alexafluor 488. These studies revealed binding to galacto-N-biose, consistent with a role for these domains in localizing the enzyme near its substrates.
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Affiliation(s)
- Lisa M Willis
- Glycobiology Program, Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
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21
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Morley TJ, Willis LM, Whitfield C, Wakarchuk WW, Withers SG. A new sialidase mechanism: bacteriophage K1F endo-sialidase is an inverting glycosidase. J Biol Chem 2009; 284:17404-10. [PMID: 19411257 PMCID: PMC2719380 DOI: 10.1074/jbc.m109.003970] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages specific for Escherichia coli K1 express a tailspike protein that degrades the polysialic acid coat of E. coli K1 that is essential for bacteriophage infection. This enzyme is specific for polysialic acid and is a member of a family of endo-sialidases. This family is unusual because all other previously reported sialidases outside of this family are exo- or trans-sialidases. The recently determined structure of an endo-sialidase derived from bacteriophage K1F (endoNF) revealed an active site that lacks a number of the residues that are conserved in other sialidases, implying a new, endo-sialidase-specific catalytic mechanism. Using synthetic trifluoromethylumbelliferyl oligosialoside substrates, kinetic parameters for hydrolysis at a single cleavage site were determined. Measurement of kcat/Km at a series of pH values revealed a dependence on a single protonated group of pKa 5. Mutation of a putative active site acidic residue, E581A, resulted in complete loss of sialidase activity. Direct 1H NMR analysis of the hydrolysis of trifluoromethylumbelliferyl sialotrioside revealed that endoNF is an inverting sialidase. All other wild type sialidases previously reported are retaining glycosidases, implying a new mechanism of sialidase action specific to this family of endo-sialidases.
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Affiliation(s)
- Thomas J. Morley
- From the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1
| | - Lisa M. Willis
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, and
| | - Chris Whitfield
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, and
| | - Warren W. Wakarchuk
- the Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Stephen G. Withers
- From the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1
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22
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Yang MT, Woerpel KA. The effect of electrostatic interactions on conformational equilibria of multiply substituted tetrahydropyran oxocarbenium ions. J Org Chem 2009; 74:545-53. [PMID: 19072093 DOI: 10.1021/jo8017846] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The three-dimensional structures of dioxocarbenium ions related to glycosyl cations were determined by an analysis of spectroscopic, computational, and reactivity data. Hypothetical low-energy structures of the dioxocarbenium ions were correlated with both experimentally determined (1)H NMR coupling constants and diastereoselectivity results from nucleophilic substitution reactions. This method confirmed the pseudoaxial preference of C-3 alkoxy-substituted systems and revealed the conformational preference of the C-5 alkoxymethyl group. Although the monosubstituted C-5 alkoxymethyl substituent preferred a pseudoequatorial orientation, the C-5-C-6 bond rotation was controlled by an electrostatic effect. The preferred diaxial conformer of the trans-4,5-disubstituted tetrahydropyranyl system underscored the importance of electrostatic effects in dictating conformational equilibria. In the 2-deoxymannose system, although steric effects influenced the orientation of the C-5 alkoxymethyl substituent, the all-axial conformer was favored because of electrostatic stabilization.
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Affiliation(s)
- Michael T Yang
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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23
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Abbott DW, Macauley MS, Vocadlo DJ, Boraston AB. Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases. J Biol Chem 2009; 284:11676-89. [PMID: 19181667 DOI: 10.1074/jbc.m809663200] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endo-beta-d-glucosaminidases from family 85 of glycoside hydrolases (GH85 endohexosaminidases) act to cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. Endohexosaminidase D (Endo-D), produced by Streptococcus pneumoniae, is believed to contribute to the virulence of this organism by playing a role in the deglycosylation of IgG antibodies. Endohexosaminidases have received significant attention for this reason and, moreover, because they are powerful tools for chemoenzymatic synthesis of proteins having defined glycoforms. Here we describe mechanistic and structural studies of the catalytic domain (SpGH85) of Endo-D that provide compelling support for GH85 enzymes using a catalytic mechanism involving substrate-assisted catalysis. Furthermore, the structure of SpGH85 in complex with the mechanism-based competitive inhibitor NAG-thiazoline (K(d) = 28 microm) provides a coherent rationale for previous mutagenesis studies of Endo-D and other related GH85 enzymes. We also find GH85, GH56, and GH18 enzymes have a similar configuration of catalytic residues. Notably, GH85 enzymes have an asparagine in place of the aspartate residue found in these other families of glycosidases. We propose that this residue, as the imidic acid tautomer, acts analogously to the key catalytic aspartate of GH56 and GH18 enzymes. This topographically conserved arrangement of the asparagine residue and a conserved glutamic acid, coupled with previous kinetic studies, suggests these enzymes may use an unusual proton shuttle to coordinate effective general acid and base catalysis to aid cleavage of the glycosidic bond. These results collectively provide a blueprint that may be used to facilitate protein engineering of these enzymes to improve their function as biocatalysts for synthesizing glycoproteins having defined glycoforms and also may serve as a guide for generating inhibitors of GH85 enzymes.
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Affiliation(s)
- D Wade Abbott
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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24
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Ibatullin FM, Baumann MJ, Greffe L, Brumer H. Kinetic Analyses of Retaining endo-(Xylo)glucanases from Plant and Microbial Sources Using New Chromogenic Xylogluco-Oligosaccharide Aryl Glycosides. Biochemistry 2008; 47:7762-9. [DOI: 10.1021/bi8009168] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Farid M. Ibatullin
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Martin J. Baumann
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Lionel Greffe
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Harry Brumer
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
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25
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Hekmat O, He S, Warren RAJ, Withers SG. A Mechanism-Based ICAT Strategy for Comparing Relative Expression and Activity Levels of Glycosidases in Biological Systems. J Proteome Res 2008; 7:3282-92. [DOI: 10.1021/pr7008302] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Omid Hekmat
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - Shouming He
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - R. Antony J. Warren
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1, and Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., Canada, V6T 1Z3
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26
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Hekmat O, Florizone C, Kim YW, Eltis LD, Warren RAJ, Withers SG. Specificity Fingerprinting of Retaining β-1,4-Glycanases in theCellulomonas fimi Secretome Using Two Fluorescent Mechanism-Based Probes. Chembiochem 2007; 8:2125-32. [DOI: 10.1002/cbic.200700481] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Chen HM, Withers SG. Facile synthesis of 2,4-dinitrophenyl alpha-D-glycopyranosides as chromogenic substrates for alpha-glycosidases. Chembiochem 2007; 8:719-22. [PMID: 17373018 DOI: 10.1002/cbic.200700021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hong-Ming Chen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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28
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Gloster TM, Ibatullin FM, Macauley K, Eklöf JM, Roberts S, Turkenburg JP, Bjørnvad ME, Jørgensen PL, Danielsen S, Johansen KS, Borchert TV, Wilson KS, Brumer H, Davies GJ. Characterization and Three-dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families GH5 and GH12. J Biol Chem 2007; 282:19177-89. [PMID: 17376777 DOI: 10.1074/jbc.m700224200] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The plant cell wall is a complex material in which the cellulose microfibrils are embedded within a mesh of other polysaccharides, some of which are loosely termed "hemicellulose." One such hemicellulose is xyloglucan, which displays a beta-1,4-linked d-glucose backbone substituted with xylose, galactose, and occasionally fucose moieties. Both xyloglucan and the enzymes responsible for its modification and degradation are finding increasing prominence, reflecting both the drive for enzymatic biomass conversion, their role in detergent applications, and the utility of modified xyloglucans for cellulose fiber modification. Here we present the enzymatic characterization and three-dimensional structures in ligand-free and xyloglucan-oligosaccharide complexed forms of two distinct xyloglucanases from glycoside hydrolase families GH5 and GH12. The enzymes, Paenibacillus pabuli XG5 and Bacillus licheniformis XG12, both display open active center grooves grafted upon their respective (beta/alpha)(8) and beta-jelly roll folds, in which the side chain decorations of xyloglucan may be accommodated. For the beta-jelly roll enzyme topology of GH12, binding of xylosyl and pendant galactosyl moieties is tolerated, but the enzyme is similarly competent in the degradation of unbranched glucans. In the case of the (beta/alpha)(8) GH5 enzyme, kinetically productive interactions are made with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides. The differential strategies for the accommodation of the side chains of xyloglucan presumably facilitate the action of these microbial hydrolases in milieus where diverse and differently substituted substrates may be encountered.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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29
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Wicki J, Williams SJ, Withers SG. Transition-State Mimicry by Glycosidase Inhibitors: A Critical Kinetic Analysis. J Am Chem Soc 2007; 129:4530-1. [PMID: 17385869 DOI: 10.1021/ja0707254] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jacqueline Wicki
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, Canada V6T 1Z1
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30
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Williams SJ, Hekmat O, Withers SG. Synthesis and Testing of Mechanism-Based Protein-Profiling Probes for Retaining Endo-glycosidases. Chembiochem 2006; 7:116-24. [PMID: 16397879 DOI: 10.1002/cbic.200500279] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New functional proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Glycosidases play critical roles in biology, yet a robust method for functional analysis of their activities and identities in biological proteomes is still lacking. An aryl 2-deoxy-2-fluoro xylobioside inactivator was conjugated through cleavable and noncleavable linker arms to a biotin tag, thereby yielding two new active-site-directed reagents for activity-based profiling of retaining beta-glycanases in complex proteomes. Crucially, these tagged reagents possess high specificity for their target enzymes with kinetic parameters similar to those of the untagged reagent. Western blotting showed that these reagents bind and covalently label active retaining beta-glycanases both in pure enzyme samples and in the secreted proteome of the soil bacterium Cellulomonas fimi. Such reagents therefore show great promise for future activity-based targeting of glycanases.
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Affiliation(s)
- Spencer J Williams
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
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31
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Hekmat O, Kim YW, Williams SJ, He S, Withers SG. Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi. J Biol Chem 2005; 280:35126-35. [PMID: 16085650 DOI: 10.1074/jbc.m508434200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
New proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Here, we report the first gel-free, mass spectrometry-based strategy for mechanism-based profiling of retaining beta-endoglycosidases in complex proteomes. Using a biotinylated, cleavable 2-deoxy-2-fluoroxylobioside inactivator, we have isolated and identified the active-site peptides of target retaining beta-1,4-glycanases in systems of increasing complexity: pure enzymes, artificial proteomes, and the secreted proteome of the aerobic mesophilic soil bacterium Cellulomonas fimi. The active-site peptide of a new C. fimi beta-1,4-glycanase was identified in this manner, and the peptide sequence, which includes the catalytic nucleophile, is highly conserved among glycosidase family 10 members. The glycanase gene (GenBank accession number DQ146941) was cloned using inverse PCR techniques, and the protein was found to comprise a catalytic domain that shares approximately 70% sequence identity with those of xylanases from Streptomyces sp. and a family 2b carbohydrate-binding module. The new glycanase hydrolyzes natural and artificial xylo-configured substrates more efficiently than their cello-configured counterparts. It has a pH dependence very similar to that of known C. fimi retaining glycanases.
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Affiliation(s)
- Omid Hekmat
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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32
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Kipper K, Väljamäe P, Johansson G. Processive action of cellobiohydrolase Cel7A from Trichoderma reesei is revealed as 'burst' kinetics on fluorescent polymeric model substrates. Biochem J 2005; 385:527-35. [PMID: 15362979 PMCID: PMC1134725 DOI: 10.1042/bj20041144] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Reaction conditions for the reducing-end-specific derivatization of cellulose substrates with the fluorogenic compound, anthranilic acid, have been established. Hydrolysis of fluorescence-labelled celluloses by cellobiohydrolase Cel7A from Trichoderma reesei was consistent with the active-site titration kinetics (burst kinetics), which allowed the quantification of the processivity of the enzyme. The processivity values of 88+/-10, 42+/-10 and 34+/-2.0 cellobiose units were found for Cel7A acting on labelled bacterial cellulose, bacterial microcrystalline cellulose and endoglucanase-pretreated bacterial cellulose respectively. The anthranilic acid derivatization also provides an alternative means for estimating the average degree of polymerization of cellulose and, furthermore, allows the quantitative monitoring of the production of reducing end groups on solid cellulose on hydrolysis by cellulases. Hydrolysis of bacterial cellulose by cellulases from T. reesei revealed that, by contrast with endoglucanase Cel5A, neither cellobiohydrolases Cel7A nor Cel6A produced detectable amounts of new reducing end groups on residual cellulose.
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Affiliation(s)
- Kalle Kipper
- *Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Priit Väljamäe
- *Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
- To whom correspondence should be addressed (email )
| | - Gunnar Johansson
- †Department of Biochemistry, University of Uppsala, P.O. Box 576, S-75 123 Uppsala, Sweden
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33
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Vocadlo DJ, Withers SG. The chemical synthesis of 2-deoxy-2-fluorodisaccharide probes of the hen egg white lysozyme mechanism. Carbohydr Res 2005; 340:379-88. [PMID: 15680592 DOI: 10.1016/j.carres.2004.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2004] [Revised: 12/11/2004] [Accepted: 12/14/2004] [Indexed: 11/16/2022]
Abstract
2,4-Dinitrophenyl 2-acetamido-2-deoxy-beta-d-glucopyranosyl-(1-->4)-2-deoxy-2-fluoro-beta-d-glucopyranoside (GN2FG-DNP) and 2-acetamido-2-deoxy-beta-d-glucopyranosyl-(1-->4)-2-deoxy-2-fluoro-beta-d-glucopyranosyl fluoride (GN2FG-F) were prepared using a divergent synthetic approach involving 10 steps. The key steps involved the preparation of 1-O-acetyl-3,6-di-O-benzyl-2-deoxy-2-fluoro-alpha/beta-d-glucopyranose using Selectfluor(trade mark) in the presence of acetic acid and the subsequent glycosylation of this acceptor to generate the core 2-fluorodisaccharide. After further elaboration, the target molecules were obtained and tested as probes of the mechanism of hen egg white lysozyme (HEWL). Compound GN2FG-DNP is not a substrate for the enzyme while compound GN2FG-F is cleaved slowly with an apparent K(m) greater than 5mM and a second-order rate constant of k(cat)/K(m)=9.6s(-1)M(-1). Comparison of this value to that estimated for the hydrolysis of beta-chitobiosyl fluoride by HEWL (1200s(-1)M(-1)) [Ballardie, F. W.; Capon, B.; Cuthbert, M. W.; Dearie, W. M. Bioorg. Chem.1977, 6, 483-509] revealed a 126-fold rate decrease upon substitution of a fluorine group for the 2-acetamido group of beta-chitobiosyl fluoride. This decrease resulted in the steady-state accumulation of an intermediate as visualized by mass spectrometry and the ultimate crystallographic determination of its structure [Vocadlo, D. J.; Davies, G. J.; Laine, R.; Withers, S. G. Nature2001, 412, 835-838].
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Affiliation(s)
- David J Vocadlo
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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Abstract
Cellulomonas is a unique bacterium possessing not only the capacity to degrade various carbohydrates, such as starch, xylan and cellulose, but crystalline cellulose as well. It has developed a complex battery of glucanases to deal with substrates possessing such extensive microheterogeneities. Some of these enzymes are multifunctional, as well as cross inducible, possessing a multi-domain structure; these enzymes are thought to have arisen by the shuffling of these domains. Intergeneric hybrids have been constructed between Cellulomonas and Zymomonas so as to enhance the industrial potential of this organism. This review examines the unique features of this microorganism and evaluates its key role in the conversion of complex wastes to useful products, by virtue of its unusual attributes.
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Affiliation(s)
- P Chaudhary
- Molecular Biology Research Laboratory, Department of Zoology, University of Poona, Pune-411 007, India
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35
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Pell G, Szabo L, Charnock SJ, Xie H, Gloster TM, Davies GJ, Gilbert HJ. Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J Biol Chem 2003; 279:11777-88. [PMID: 14670951 DOI: 10.1074/jbc.m311947200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbial degradation of the plant cell wall is the primary mechanism by which carbon is utilized in the biosphere. The hydrolysis of xylan, by endo-beta-1,4-xylanases (xylanases), is one of the key reactions in this process. Although amino acid sequence variations are evident in the substrate binding cleft of "family GH10" xylanases (see afmb.cnrs-mrs.fr/CAZY/), their biochemical significance is unclear. The Cellvibrio japonicus GH10 xylanase CjXyn10C is a bi-modular enzyme comprising a GH10 catalytic module and a family 15 carbohydrate-binding module. The three-dimensional structure at 1.85 A, presented here, shows that the sequence joining the two modules is disordered, confirming that linker sequences in modular glycoside hydrolases are highly flexible. CjXyn10C hydrolyzes xylan at a rate similar to other previously described GH10 enzymes but displays very low activity against xylooligosaccharides. The poor activity on short substrates reflects weak binding at the -2 subsite of the enzyme. Comparison of CjXyn10C with other family GH10 enzymes reveals "polymorphisms" in the substrate binding cleft including a glutamate/glycine substitution at the -2 subsite and a tyrosine insertion in the -2/-3 glycone region of the substrate binding cleft, both of which contribute to the unusual properties of the enzyme. The CjXyn10C-substrate complex shows that Tyr-340 stacks against the xylose residue located at the -3 subsite, and the properties of Y340A support the view that this tyrosine plays a pivotal role in substrate binding at this location. The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed.
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Affiliation(s)
- Gavin Pell
- School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, The Agriculture Bldg., Newcastle upon Tyne NE1 7RU
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Wejse PL, Ingvorsen K, Mortensen KK. Purification and characterisation of two extremely halotolerant xylanases from a novel halophilic bacterium. Extremophiles 2003; 7:423-31. [PMID: 12884087 DOI: 10.1007/s00792-003-0342-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Accepted: 06/10/2003] [Indexed: 11/25/2022]
Abstract
The present work reports for the first time the purification and characterisation of two extremely halotolerant endo-xylanases from a novel halophilic bacterium, strain CL8. Purification of the two xylanases, Xyl 1 and 2, was achieved by anion exchange and hydrophobic interaction chromatography. The enzymes had relative molecular masses of 43 kDa and 62 kDa and pI of 5.0 and 3.4 respectively. Stimulation of activity by Ca(2+), Mn(2+), Mg(2+), Ba(2+), Li(2+), NaN(3) and isopropanol was observed. The K(m) and V(max) values determined for Xyl 1 with 4- O-methyl- d-glucuronoxylan are 5 mg/ml and 125,000 nkat/mg respectively. The corresponding values for Xyl 2 were 1 mg/ml and 143,000 nkat/mg protein. Xylobiose and xylotriose were the major end products for both endoxylanases. The xylanases were stable at pH 4-11 showing pH optima around pH 6. Xyl 1 shows maximal activity at 60 degrees C, Xyl 2 at 65 degrees C (at 4 M NaCl). The xylanases showed high temperature stability with half-lives at 60 degrees C of 97 min and 192 min respectively. Both xylanases showed optimal activity at 1 M NaCl, but substantial activity remained for both enzymes at 5 M NaCl.
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Affiliation(s)
- Peter Langborg Wejse
- Department of Microbial Ecology, Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 540, 8000 Aarhus, Denmark
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37
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Vincent F, Charnock SJ, Verschueren KHG, Turkenburg JP, Scott DJ, Offen WA, Roberts S, Pell G, Gilbert HJ, Davies GJ, Brannigan JA. Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9A resolution. J Mol Biol 2003; 330:593-606. [PMID: 12842474 DOI: 10.1016/s0022-2836(03)00632-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C. The 1.9A structure of the multifunctional CE-7 esterase (hereinafter CAH) from Bacillus subtilis 168 reveals a classical alpha/beta hydrolase fold encased within a 32 hexamer. This is the first example of a hexameric alpha/beta hydrolase and is further evidence of the versatility of this particular fold, which is used in a wide variety of biological contexts. A narrow entrance tunnel leads to the centre of the molecule, where the six active-centre catalytic triads point towards the tunnel interior and thus are sequestered away from cytoplasmic contents. By analogy to self-compartmentalising proteases, the tunnel entrance may function to hinder access of large substrates to the poly-specific active centre. This would explain the observation that the enzyme is active on a variety of small, acetylated molecules. The structure of an active site mutant in complex with the reaction product, acetate, reveals details of the putative oxyanion binding site, and suggests that substrates bind predominantly through non-specific contacts with protein hydrophobic residues. Protein residues involved in catalysis are tethered by interactions with protein excursions from the canonical alpha/beta hydrolase fold. These excursions also mediate quaternary structure maintenance, so it would appear that catalytic competence is only achieved on protein multimerisation. We suggest that the acetyl xylan esterase (EC 3.1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates.
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Affiliation(s)
- Florence Vincent
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
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38
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Ducros VMA, Tarling CA, Zechel DL, Brzozowski AM, Frandsen TP, von Ossowski I, Schülein M, Withers SG, Davies GJ. Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants. CHEMISTRY & BIOLOGY 2003; 10:619-28. [PMID: 12890535 DOI: 10.1016/s1074-5521(03)00143-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The formation of glycoconjugates and oligosaccharides remains one of the most challenging chemical syntheses. Chemo-enzymatic routes using retaining glycosidases have been successfully harnessed but require tight kinetic or thermodynamic control. "Glycosynthases," specifically engineered glycosidases that catalyze the formation of glycosidic bonds from glycosyl donor and acceptor alcohol, are an emerging range of synthetic tools in which catalytic nucleophile mutants are harnessed together with glycosyl fluoride donors to generate powerful and versatile catalysts. Here we present the structural and kinetic dissection of the Humicola insolens Cel7B glycosynthases in which the nucleophile of the wild-type enzyme is mutated to alanine and serine (E197A and E197S). 3-D structures reveal the acceptor and donor subsites and the basis for substrate inhibition. Kinetic analysis shows that the E197S mutant is considerably more active than the corresponding alanine mutant due to a 40-fold increase in k(cat).
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Affiliation(s)
- Valérie M-A Ducros
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
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Zechel DL, Reid SP, Stoll D, Nashiru O, Warren RAJ, Withers SG. Mechanism, mutagenesis, and chemical rescue of a beta-mannosidase from cellulomonas fimi. Biochemistry 2003; 42:7195-204. [PMID: 12795616 DOI: 10.1021/bi034329j] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical mechanism of a retaining beta-mannosidase from Cellulomonas fimi has been characterized through steady-state kinetic analyses with a range of substrates, coupled with chemical rescue studies on both the wild-type enzyme and mutants in which active site carboxyl groups have been replaced. Studies with a series of aryl beta-mannosides of vastly different reactivities (pK(a)(lg) = 4-10) allowed kinetic isolation of the glycosylation and deglycosylation steps. Substrate inhibition was observed for all but the least reactive of these substrates. Brønsted analysis of k(cat) revealed a downward breaking plot (beta(lg) = -0.54 +/- 0.05) that is consistent with a change in rate-determining step (glycosylation to deglycosylation), and this was confirmed by partitioning studies with ethylene glycol. The pH dependence of k(cat)/K(m) follows an apparent single ionization of a group of pK(a) = 7.65 that must be protonated for catalysis. The tentative assignment of E429 as the acid-base catalyst of Man2A on the basis of sequence alignments with other family 2 glycosidases was confirmed by the increased turnover rate observed for the mutant E429A in the presence of azide and fluoride, leading to the production of beta-mannosyl azide and beta-mannosyl fluoride, respectively. A pH-dependent chemical rescue of E429A activity is also observed with citrate. Substantial oxocarbenium ion character at the transition state was demonstrated by the alpha-deuterium kinetic isotope effect for Man2A E429A of alpha-D(V) = 1.12 +/- 0.01. Surprisingly, this isotope effect was substantially greater in the presence of azide (alpha-D(V) = 1.166 +/- 0.009). Likely involvement of acid/base catalysis was revealed by the pH dependence of k(cat) for Man2A E429A, which follows a bell-shaped profile described by pK(a) values of 6.1 and 8.4, substantially different from that of the wild-type enzyme. The glycosidic bond cleaving activity of Man2A E519A and E519S nucleophile mutants is restored with azide and fluoride and appears to correlate with the corresponding "glycosynthase" activities. The contribution of the substrate 2-hydroxyl to stabilization of the Man2A glycosylation transition state (DeltaDeltaG() = 5.1 kcal mol(-1)) was probed using a 2-deoxymannose substrate. This value, surprisingly, is comparable to that found from equivalent studies with beta-glucosidases despite the geometric differences at C-2 and the importance of hydrogen bonding at that position. Modes of stabilizing the mannosidase transition state are discussed.
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Affiliation(s)
- David L Zechel
- PENCE and Department of Chemistry and Microbiology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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40
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Nagy T, Nurizzo D, Davies GJ, Biely P, Lakey JH, Bolam DN, Gilbert HJ. The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants. J Biol Chem 2003; 278:20286-92. [PMID: 12654910 DOI: 10.1074/jbc.m302205200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
alpha-Glucuronidases are key components of the ensemble of enzymes that degrade the plant cell wall. They hydrolyze the alpha1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid (4-O-MeGlcA) and the xylan or xylooligosaccharide backbone. Here we report the crystal structure of an inactive mutant (E292A) of the alpha-glucuronidase, GlcA67A, from Cellvibrio japonicus in complex with its substrate. The data show that the 4-O-methyl group of the substrate is accommodated within a hydrophobic sheath flanked by Val-210 and Trp-160, whereas the carboxylate moiety is located within a positively charged region of the substrate-binding pocket. The carboxylate side chains of Glu-393 and Asp-365, on the "beta-face" of 4-O-MeGlcA, form hydrogen bonds with a water molecule that is perfectly positioned to mount a nucleophilic attack at the anomeric carbon of the target glycosidic bond, providing further support for the view that, singly or together, these amino acids function as the catalytic base. The capacity of reaction products and product analogues to inhibit GlcA67A shows that the 4-O-methyl group, the carboxylate, and the xylose sugar of aldobiouronic acid all play an important role in substrate binding. Site-directed mutagenesis informed by the crystal structure of enzyme-ligand complexes was used to probe the importance of highly conserved residues at the active site of GlcA67A. The biochemical properties of K288A, R325A, and K360A show that a constellation of three basic amino acids (Lys-288, Arg-325, and Lys-360) plays a critical role in binding the carboxylate moiety of 4-O-MeGlcA. Disruption of the apolar nature of the pocket created by Val-210 (V210N and V210S) has a detrimental effect on substrate binding, although the reduction in affinity is not reflected by an inability to accommodate the 4-O-methyl group. Replacing the two tryptophan residues that stack against the sugar rings of the substrate with alanine (W160A and W543A) greatly reduced activity.
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Affiliation(s)
- Tibor Nagy
- School of Cell and Molecular Biosciences, The University of Newcastle upon Tyne, United Kingdom
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41
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Abel M, Iversen K, Planas A, Christensen U. Pre-steady-state kinetics of Bacillus licheniformis 1,3-1,4-beta-glucanase: evidence for a regulatory binding site. Biochem J 2003; 371:997-1003. [PMID: 12568655 PMCID: PMC1223346 DOI: 10.1042/bj20021504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2002] [Revised: 01/17/2003] [Accepted: 02/04/2003] [Indexed: 11/17/2022]
Abstract
In a previous paper, we reported the first stopped-flow experiments on a Bacillus licheniformis 1,3-1,4-beta-glucanase [Abel, Planas and Christensen (2001) Biochem. J. 357, 195-202]. It was shown that the pre-steady-state kinetics of the 1,3-1,4-beta-glucanase using the substrate 4-methylumbelliferyl 3-O-beta-cellobiosyl-beta-D-glucoside may be explained by a reaction scheme involving an induced fit and the binding of two substrates as well as a second enzymic conformational change, whereas the results definitely could not be explained in terms of the simple double-displacement scheme. In the present study, we report further stopped-flow kinetic results on the glucanase using a series of low-molecular-mass substrates with various leaving groups and varying chain length. The analysis of the resulting data leads to the conclusion that the free enzyme exists in two conformations, one of which binds the substrates rather strongly in a regulatory site, before any productive interactions can take place. This corresponds to an allosteric activation mechanism. With these substrates, however, the productive enzyme-substrate species are also able to change into less active or inactive forms. This may be seen as a feedback inhibitory mechanism.
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Affiliation(s)
- Mireia Abel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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42
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Abstract
The mechanism-based inactivation and subsequent identification of the nucleophilic residue using mass spectrometry have been successfully applied and used to identify the active-site nucleophile in numerous beta-glycosidases, as illustrated using C. fimi exoglycanase. Evidence for a covalent glycosyl-enzyme intermediate has come from X-ray crystallographic analysis of trapped complexes, the first being that of the trapped fluoroglycosyl-enzyme intermediate of Cex. The crystal structure of the trapped fluorocellobiosyl-enzyme complex for Cex has provided useful insights into catalysis and the roles of specific residues at the active site. In addition, information about the conformation of the natural sugar in the covalently bound state and the interactions at the active site was obtained using a mutant form of Cex.
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Affiliation(s)
- Jacqueline Wicki
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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43
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Desmet T, Nerinckx W, Stals I, Callewaert N, Contreras R, Claeyssens M. Novel tools for the study of class I alpha-mannosidases: a chromogenic substrate and a substrate-analog inhibitor. Anal Biochem 2002; 307:361-7. [PMID: 12202255 DOI: 10.1016/s0003-2697(02)00039-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of chromogenic substrates for evaluation of class I alpha-mannosidase is described. 2('),4(')-Dinitrophenyl-alpha-D-mannopyranoside allows rapid and sensitive assays of enzymatic activities, e.g., of heterologously expressed alpha-1,2-mannosidase from Trichoderma reesei. Interaction constants of several ligands with alpha-mannosidases from class I and II could also be determined. Furthermore, novel types of inhibitors derived from D-lyxose are presented. Methyl-alpha-D-lyxopyranosyl-(1(')-->2)-alpha-D-mannopyranoside is a potent inhibitor of the alpha-1,2-mannosidase from T. reesei (K(i)=600 microM) and since it probably spans subsites -1/+1, this disaccharide could be valuable in crystallographic studies of class I alpha-mannosidases.
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Affiliation(s)
- T Desmet
- Laboratory for Biochemistry, Department of Biochemistry, Physiology, and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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44
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Honda Y, Kitaoka M, Sakka K, Ohmiya K, Hayashi K. An investigation of the pH-activity relationships of Cex, a family 10 xylanase from Cellulomonas fimi: xylan inhibition and the influence of nitro-substituted aryl-β-d-xylobiosides on xylanase activity. J Biosci Bioeng 2002. [DOI: 10.1016/s1389-1723(02)80034-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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45
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García-Moreno MI, Benito JM, Ortiz Mellet C, García Fernández JM. Synthesis and evaluation of calystegine B2 analogues as glycosidase inhibitors. J Org Chem 2001; 66:7604-14. [PMID: 11701011 DOI: 10.1021/jo015639f] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A practical synthesis of polyhydroxylated 6-oxa-nor-tropanes incorporating the essential structural features of calystegine B(2) from 5-deoxy-5-thioureido and 5-ureido-L-idofuranose precursors is presented. The methodology relies on the ability of pseudoamide-type nitrogen atoms (thiourea, urea, and carbamate) to undergo nucleophilic addition to the masked aldehyde group of the monosaccharide. The generated hemiaminal functionality may further undergo in situ intramolecular glycosidation to give the bicyclic aminoacetal compounds, the whole process being favored by the anomeric effect. A series of derivatives bearing different substituents at nitrogen has been prepared and screened against several glycosidases in comparison with xylonojirimycin-type piperidine analogues. Interestingly, strong and highly specific inhibition of bovine liver beta-glucosidase was observed for 6-oxacalystegine B(2) analogues incorporating aromatic pseudoaglyconic groups. On the basis of these data, a 1-azasugar inhibition mode is proposed for this family of glycomimetics.
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Affiliation(s)
- M I García-Moreno
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, E-41071 Seville, Spain
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46
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Abel M, Planas A, Christensen U. Presteady-state kinetics of Bacillus 1,3-1,4-beta-glucanase: binding and hydrolysis of a 4-methylumbelliferyl trisaccharide substrate. Biochem J 2001; 357:195-202. [PMID: 11415449 PMCID: PMC1221941 DOI: 10.1042/0264-6021:3570195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present study the first stopped-flow experiments performed on Bacillus 1,3-1,4-beta-glucanases are reported. The presteady-state kinetics of the binding of 4-methylumbelliferyl 3-O-beta-cellobiosyl-beta-D-glucoside to the inactive mutant E134A, and the wild-type-catalysed hydrolysis of the same substrate, were studied by measuring changes in the fluorescence of bound substrate or 4-methylumbelliferone produced. The presteady-state traces all showed an initial lag phase followed by a fast monoexponential phase leading to equilibration (for binding to E134A) or to steady state product formation (for the wild-type reaction). The lag phase, with a rate constant of the order of 100 s(-1), was independent of the substrate concentration; apparently an induced-fit mechanism governs the formation of enzyme-substrate complexes. The concentration dependencies of the observed rate constant of the second presteady-state phase were analysed according to a number of reaction models. For the reaction of the wild-type enzyme, it is shown that the fast product formation observed before steady state is not due to a rate-determining deglycosylation step. A model that can explain the observed results involves, in addition to the induced fit, a conformational change of the productive ES complex into a form that binds a second substrate molecule in a non-productive mode.
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Affiliation(s)
- M Abel
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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47
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Viladot JL, Canals F, Batllori X, Planas A. Long-lived glycosyl-enzyme intermediate mimic produced by formate re-activation of a mutant endoglucanase lacking its catalytic nucleophile. Biochem J 2001; 355:79-86. [PMID: 11256951 PMCID: PMC1221714 DOI: 10.1042/0264-6021:3550079] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mutant E134A 1,3-1,4-beta-glucanase from Bacillus licheniformis, in which the catalytic nucleophilic residue has been removed by mutation to alanine, has its hydrolytic activity rescued by exogenous formate in a concentration-dependent manner. A long-lived alpha-glycosyl formate is detected and identified by (1)H-NMR and matrix-assisted laser desorption ionization-time-of-flight-MS. The intermediate is kinetically competent, since it is, at least partially, enzymically hydrolysed, and able to act as a glycosyl donor in transglycosylation reactions. This transient compound represents a true covalent glycosyl-enzyme intermediate mimic of the proposed covalent intermediate in the reaction mechanism of retaining glycosidases.
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Affiliation(s)
- J L Viladot
- Laboratori de Bioquímica, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain
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48
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Planas A. Bacterial 1,3-1,4-beta-glucanases: structure, function and protein engineering. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1543:361-382. [PMID: 11150614 DOI: 10.1016/s0167-4838(00)00231-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
1,3-1,4-beta-Glucanases (or lichenases, EC 3.2.1.73) hydrolyse linear beta-glucans containing beta-1,3 and beta-1,4 linkages such as cereal beta-glucans and lichenan, with a strict cleavage specificity for beta-1,4 glycosidic bonds on 3-O-substituted glucosyl residues. The bacterial enzymes are retaining glycosyl hydrolases of family 16 with a jellyroll beta-sandwich fold and a substrate binding cleft composed of six subsites. The present paper reviews the structure-function aspects of the enzymatic action including mechanistic enzymology, protein engineering and X-ray crystallographic studies.
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Affiliation(s)
- A Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta, 390, 08017, Barcelona, Spain.
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49
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Leggio LL, Jenkins J, Harris GW, Pickersgill RW. X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A. Proteins 2000; 41:362-73. [PMID: 11025547 DOI: 10.1002/1097-0134(20001115)41:3<362::aid-prot80>3.0.co;2-n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure of the complex between a catalytically compromised family 10 xylanase and a xylopentaose substrate has been determined by X-ray crystallography and refined to 3.2 A resolution. The substrate binds at the C-terminal end of the eightfold betaalpha-barrel of Pseudomonas fluorescens subsp. cellulosa xylanase A and occupies substrate binding subsites -1 to +4. Crystal contacts are shown to prevent the expected mode of binding from subsite -2 to +3, because of steric hindrance to subsite -2. The loss of accessible surface at individual subsites on binding of xylopentaose parallels well previously reported experimental measurements of individual subsites binding energies, decreasing going from subsite +2 to +4. Nine conserved residues contribute to subsite -1, including three tryptophan residues forming an aromatic cage around the xylosyl residue at this subsite. One of these, Trp 313, is the single residue contributing most lost accessible surface to subsite -1, and goes from a highly mobile to a well-defined conformation on binding of the substrate. A comparison of xylanase A with C. fimi CEX around the +1 subsite suggests that a flatter and less polar surface is responsible for the better catalytic properties of CEX on aryl substrates. The view of catalysis that emerges from combining this with previously published work is the following: (1) xylan is recognized and bound by the xylanase as a left-handed threefold helix; (2) the xylosyl residue at subsite -1 is distorted and pulled down toward the catalytic residues, and the glycosidic bond is strained and broken to form the enzyme-substrate covalent intermediate; (3) the intermediate is attacked by an activated water molecule, following the classic retaining glycosyl hydrolase mechanism.
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Affiliation(s)
- L L Leggio
- Centre for Crystallographic Studies, Chemical Institute, University of Copenhagen, Copenhagen, Denmark.
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Joshi MD, Sidhu G, Pot I, Brayer GD, Withers SG, McIntosh LP. Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J Mol Biol 2000; 299:255-79. [PMID: 10860737 DOI: 10.1006/jmbi.2000.3722] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pH optima of family 11 xylanases are well correlated with the nature of the residue adjacent to the acid/base catalyst. In xylanases that function optimally under acidic conditions, this residue is aspartic acid, whereas it is asparagine in those that function under more alkaline conditions. Previous studies of wild-type (WT) Bacillus circulans xylanase (BCX), with an asparagine residue at position 35, demonstrated that its pH-dependent activity follows the ionization states of the nucleophile Glu78 (pKa 4.6) and the acid/base catalyst Glu172 (pKa 6.7). As predicted from sequence comparisons, substitution of this asparagine residue with an aspartic acid residue (N35D BCX) shifts its pH optimum from 5.7 to 4.6, with an approximately 20% increase in activity. The bell-shaped pH-activity profile of this mutant enzyme follows apparent pKa values of 3.5 and 5.8. Based on 13C-NMR titrations, the predominant pKa values of its active-site carboxyl groups are 3.7 (Asp35), 5.7 (Glu78) and 8.4 (Glu172). Thus, in contrast to the WT enzyme, the pH-activity profile of N35D BCX appears to be set by Asp35 and Glu78. Mutational, kinetic, and structural studies of N35D BCX, both in its native and covalently modified 2-fluoro-xylobiosyl glycosyl-enzyme intermediate states, reveal that the xylanase still follows a double-displacement mechanism with Glu78 serving as the nucleophile. We therefore propose that Asp35 and Glu172 function together as the general acid/base catalyst, and that N35D BCX exhibits a "reverse protonation" mechanism in which it is catalytically active when Asp35, with the lower pKa, is protonated, while Glu78, with the higher pKa, is deprotonated. This implies that the mutant enzyme must have an inherent catalytic efficiency at least 100-fold higher than that of the parental WT, because only approximately 1% of its population is in the correct ionization state for catalysis at its pH optimum. The increased efficiency of N35D BCX, and by inference all "acidic" family 11 xylanases, is attributed to the formation of a short (2.7 A) hydrogen bond between Asp35 and Glu172, observed in the crystal structure of the glycosyl-enzyme intermediate of this enzyme, that will substantially stabilize the transition state for glycosyl transfer. Such a mechanism may be much more commonly employed than is generally realized, necessitating careful analysis of the pH-dependence of enzymatic catalysis.
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Affiliation(s)
- M D Joshi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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