201
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NI HUI, CAI HUINONG, CHEN FENG, YOU QI, XIAO ANFENG, WANG YAQI. PURIFICATION AND CHARACTERIZATION OF β-D-GLUCOSIDASE FROM ASPERGILLUS NIGER NARINGINASE. J Food Biochem 2011. [DOI: 10.1111/j.1745-4514.2011.00556.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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202
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Ni H, Chen F, Cai H, Xiao A, You Q, Lu Y. Characterization and Preparation of Aspergillus niger Naringinase for Debittering Citrus Juice. J Food Sci 2011; 77:C1-7. [DOI: 10.1111/j.1750-3841.2011.02471.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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203
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Pierdominici-Sottile G, Horenstein NA, Roitberg AE. Free energy study of the catalytic mechanism of Trypanosoma cruzi trans-sialidase. From the Michaelis complex to the covalent intermediate. Biochemistry 2011; 50:10150-8. [PMID: 22007596 DOI: 10.1021/bi2009618] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Trypanosoma cruzi trans-sialidase (TcTS) is a crucial enzyme for the infection of Trypanosoma cruzi, the protozoa responsible for Chagas' disease in humans. It catalyzes the transfer of sialic acids from the host's glycoconjugates to the parasite's glycoconjugates. Based on kinetic isotope effect (KIE) studies, a strong nucleophilic participation at the transition state could be determined, and recently, elaborate experiments used 2-deoxy-2,3-difluorosialic acid as substrate and were able to trap a long-lived covalent intermediate (CI) during the catalytic mechanism. In this paper, we compute the KIE and address the entire mechanistic pathway of the CI formation step in TcTS using computational tools. Particularly, the free energy results indicate that in the transition state there is a strong nucleophilic participation of Tyr342, and after this, the system collapsed into a stable CI. We find that there is no carbocation intermediate for this reaction. By means of the energy decomposition method, we identify the residues that have the biggest influence on catalysis. This study facilitates the understanding of the catalytic mechanism of TcTS and can serve as a guide for future inhibitor design studies.
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Affiliation(s)
- Gustavo Pierdominici-Sottile
- Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Sáenz Peña 352, B1876BXD Bernal, Argentina
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204
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Identification and characterization of the Rhizobium sp. strain GIN611 glycoside oxidoreductase resulting in the deglycosylation of ginsenosides. Appl Environ Microbiol 2011; 78:242-9. [PMID: 22020506 DOI: 10.1128/aem.06404-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using enrichment culture, Rhizobium sp. strain GIN611 was isolated as having activity for deglycosylation of a ginsenoside, compound K (CK). The purified heterodimeric protein complex from Rhizobium sp. GIN611 consisted of two subunits with molecular masses of 63.5 kDa and 17.5 kDa. In the genome, the coding sequence for the small subunit was located right after the sequence for the large subunit, with one nucleotide overlapping. The large subunit showed CK oxidation activity, and the deglycosylation of compound K was performed via oxidation of ginsenoside glucose by glycoside oxidoreductase. Coexpression of the small subunit helped soluble expression of the large subunit in recombinant Escherichia coli. The purified large subunit also showed oxidation activity against other ginsenoside compounds, such as Rb1, Rb2, Rb3, Rc, F2, CK, Rh2, Re, F1, and the isoflavone daidzin, but at a much lower rate. When oxidized CK was extracted and incubated in phosphate buffer with or without enzyme, (S)-protopanaxadiol [PPD(S)] was detected in both cases, which suggests that deglycosylation of oxidized glucose is spontaneous.
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205
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Naumoff DG. Hierarchical classification of glycoside hydrolases. BIOCHEMISTRY (MOSCOW) 2011; 76:622-35. [PMID: 21639842 DOI: 10.1134/s0006297911060022] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review deals with structural and functional features of glycoside hydrolases, a widespread group of enzymes present in almost all living organisms. Their catalytic domains are grouped into 120 amino acid sequence-based families in the international classification of the carbohydrate-active enzymes (CAZy database). At a higher hierarchical level some of these families are combined in 14 clans. Enzymes of the same clan have common evolutionary origin of their genes and share the most important functional characteristics such as composition of the active center, anomeric configuration of cleaved glycosidic bonds, and molecular mechanism of the catalyzed reaction (either inverting, or retaining). There are now extensive data in the literature concerning the relationship between glycoside hydrolase families belonging to different clans and/or included in none of them, as well as information on phylogenetic protein relationship within particular families. Summarizing these data allows us to propose a multilevel hierarchical classification of glycoside hydrolases and their homologs. It is shown that almost the whole variety of the enzyme catalytic domains can be brought into six main folds, large groups of proteins having the same three-dimensional structure and the supposed common evolutionary origin.
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Affiliation(s)
- D G Naumoff
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, 117312, Russia.
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206
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Sefton MA, Skouroumounis GK, Elsey GM, Taylor DK. Occurrence, sensory impact, formation, and fate of damascenone in grapes, wines, and other foods and beverages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:9717-46. [PMID: 21866982 DOI: 10.1021/jf201450q] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Among plant-derived odorants, damascenone is one of the most ubiquitous, sometimes occurring as an apparent natural product but more commonly occurring in processed foodstuffs and beverages. It has been widely reported as a component of alcoholic beverages, particularly of wines made from the grape Vitis vinifera . Although damascenone has one of the lowest ortho- and retronasal detection thresholds of any odorant, its contribution to the sensory properties of most products remains poorly understood. Damascenone can be formed by acid-catalyzed hydrolyses of plant-derived apocarotenoids, in both aglycon and glycoconjugated forms. These reactions can account for the formation of damascenone in some, but not all, products. In wine, damascenone can also be subject to degradation processes, particularly by reaction with sulfur dioxide.
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Affiliation(s)
- Mark A Sefton
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA 5064, Australia
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207
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Souza TACB, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MT. Structure of a novel thermostable GH51 α-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Protein Sci 2011; 20:1632-7. [PMID: 21796714 PMCID: PMC3190157 DOI: 10.1002/pro.693] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/01/2011] [Indexed: 11/09/2022]
Abstract
α-L-arabinofuranosidases (EC 3.2.1.55) participate in the degradation of a variety of L-arabinose-containing polysaccharides and interact synergistically with other hemicellulases in the production of oligosaccharides and bioconversion of lignocellulosic biomass into biofuels. In this work, the structure of a novel thermostable family 51 (GH51) α-L-arabinofuranosidase from Thermotoga petrophila RKU-1 (TpAraF) was determined at 3.1 Å resolution. The TpAraF tertiary structure consists of an (α/β)-barrel catalytic core associated with a C-terminal β-sandwich domain, which is stabilized by hydrophobic contacts. In contrast to other structurally characterized GH51 AraFs, the accessory domain of TpAraF is intimately linked to the active site by a long β-hairpin motif, which modifies the catalytic cavity in shape and volume. Sequence and structural analyses indicate that this motif is unique to Thermotoga AraFs. Small angle X-ray scattering investigation showed that TpAraF assembles as a hexamer in solution and is preserved at the optimum catalytic temperature, 65°C, suggesting functional significance. Crystal packing analysis shows that the biological hexamer encompasses a dimer of trimers and the multiple oligomeric interfaces are predominantly fashioned by polar and electrostatic contacts.
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Affiliation(s)
- Tatiana ACB Souza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Camila R Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Angelica R Souza
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Daiane P Oldiges
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Rolf A Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State UniversityStillwater, Oklahoma
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
| | - Mario T Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e MateriaisCampinas, São Paulo, Brazil
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208
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209
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Naumoff DG, Stepuschenko OO. Endo-α-1,4-polygalactosaminidases and their homologs: Structure and evolution. Mol Biol 2011. [DOI: 10.1134/s0026893311030113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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210
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Fredslund F, Hachem MA, Larsen RJ, Sørensen PG, Coutinho PM, Lo Leggio L, Svensson B. Crystal structure of α-galactosidase from Lactobacillus acidophilus NCFM: insight into tetramer formation and substrate binding. J Mol Biol 2011; 412:466-80. [PMID: 21827767 DOI: 10.1016/j.jmb.2011.07.057] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
Abstract
Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of α-galactosidases (α-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized. Here, the crystal structure of α-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.58-Å-resolution crystallographic complex with α-d-galactose at substrate binding subsite -1 was determined. LaMel36A has a large N-terminal twisted β-sandwich domain, connected by a long α-helix to the catalytic (β/α)(8)-barrel domain, and a C-terminal β-sheet domain. Four identical monomers form a tightly packed tetramer where three monomers contribute to the structural integrity of the active site in each monomer. Structural comparison of LaMel36A with the monomeric Thermotoga maritima α-Gal (TmGal36A) reveals that O2 of α-d-galactose in LaMel36A interacts with a backbone nitrogen in a glycine-rich loop of the catalytic domain, whereas the corresponding atom in TmGal36A is from a tryptophan side chain belonging to the N-terminal domain. Thus, two distinctly different structural motifs participate in substrate recognition. The tetrameric LaMel36A furthermore has a much deeper active site than the monomeric TmGal36A, which possibly modulates substrate specificity. Sequence analysis of GH36, inspired by the observed structural differences, results in four distinct subgroups having clearly different active-site sequence motifs. This novel subdivision incorporates functional and architectural features and may aid further biochemical and structural analyses within GH36.
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Affiliation(s)
- Folmer Fredslund
- Department of Systems Biology, Enzyme and Protein Chemistry, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
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211
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Identification and characterization of a new naringinase-producing strain, Williopsis californica Jmudeb007. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0766-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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212
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Yan S, Li T, Yao L. Mutational Effects on the Catalytic Mechanism of Cellobiohydrolase I from Trichoderma reesei. J Phys Chem B 2011; 115:4982-9. [DOI: 10.1021/jp200384m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Shihai Yan
- Key Lab of Biofuels, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Tong Li
- Key Lab of Biofuels, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Lishan Yao
- Key Lab of Biofuels, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
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213
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Kovalevsky AY, Hanson BL, Seaver S, Fisher SZ, Mustyakimov M, Langan P. Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:283-6. [PMID: 21301107 PMCID: PMC3034629 DOI: 10.1107/s174430911005075x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/14/2010] [Indexed: 11/11/2022]
Abstract
Room-temperature X-ray and neutron diffraction data were measured from a family 11 endoxylanase holoenzyme (XynII) originating from the filamentous fungus Trichoderma longibrachiatum to 1.55 Å resolution using a home source and to 1.80 Å resolution using the Protein Crystallography Station at LANSCE. Crystals of XynII, which is an important enzyme for biofuel production, were grown at pH 8.5 in order to examine the effect of basic conditions on the protonation-state distribution in the active site and throughout the protein molecule and to provide insights for rational engineering of catalytically improved XynII for industrial applications.
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Affiliation(s)
- Andrey Y Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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214
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215
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Seiboth B, Metz B. Fungal arabinan and L-arabinose metabolism. Appl Microbiol Biotechnol 2011; 89:1665-73. [PMID: 21212945 PMCID: PMC3044236 DOI: 10.1007/s00253-010-3071-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 12/04/2022]
Abstract
l-Arabinose is the second most abundant pentose beside d-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon and energy sources has accelerated research to investigate the potential of l-arabinose for the development and production of biofuels and other bioproducts. Fungi produce a number of extracellular arabinanases, including α-l-arabinofuranosidases and endo-arabinanases, to specifically release l-arabinose from the plant polymers. Following uptake of l-arabinose, its intracellular catabolism follows a four-step alternating reduction and oxidation path, which is concluded by a phosphorylation, resulting in d-xylulose 5-phosphate, an intermediate of the pentose phosphate pathway. The genes and encoding enzymes l-arabinose reductase, l-arabinitol dehydrogenase, l-xylulose reductase, xylitol dehydrogenase, and xylulokinase of this pathway were mainly characterized in the two biotechnological important fungi Aspergillus niger and Trichoderma reesei. Analysis of the components of the l-arabinose pathway revealed a number of specific adaptations in the enzymatic and regulatory machinery towards the utilization of l-arabinose. Further genetic and biochemical analysis provided evidence that l-arabinose and the interconnected d-xylose pathway are also involved in the oxidoreductive degradation of the hexose d-galactose.
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Affiliation(s)
- Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Wien, Austria.
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216
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Stütz AE, Wrodnigg TM. Imino sugars and glycosyl hydrolases: historical context, current aspects, emerging trends. Adv Carbohydr Chem Biochem 2011; 66:187-298. [PMID: 22123190 DOI: 10.1016/b978-0-12-385518-3.00004-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty years of discoveries and research on imino sugars, which are carbohydrate analogues having a basic nitrogen atom instead of oxygen in the sugar ring and, acting as potent glycosidase inhibitors, have made considerable impact on our contemporary understanding of glycosidases. Imino sugars have helped to elucidate the catalytic machinery of glycosidases and have refined our methods and concepts of utilizing them. A number of new aspects have emerged for employing imino sugars as pharmaceutical compounds, based on their profound effects on metabolic activities in which glycosidases are involved. From the digestion of starch to the fight against viral infections, from research into malignant diseases to potential improvements in hereditary storage disorders, glycosidase action and inhibition are essential issues. This account aims at combining general developments with a focus on some niches where imino sugars have become useful tools for glycochemistry and glycobiology.
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Affiliation(s)
- Arnold E Stütz
- Institut für Organische Chemie, Technische Universität Graz, Austria
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217
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Gazit OM, Charmot A, Katz A. Grafted cellulose strands on the surface of silica: effect of environment on reactivity. Chem Commun (Camb) 2011; 47:376-8. [DOI: 10.1039/c0cc02105a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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218
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Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C. Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem 2010; 285:35675-84. [PMID: 20826810 PMCID: PMC2975192 DOI: 10.1074/jbc.m110.131037] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 09/03/2010] [Indexed: 11/06/2022] Open
Abstract
Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain β-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-Å resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-β-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and β-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within β-N-acetylglucosaminidases but otherwise absent in β-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 β-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of β-lactamase.
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Affiliation(s)
| | - Stefanie Fischer
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Patrick Polzer
- the Max-Planck-Institute of Quantum Optics, 85748 Garching, Germany
| | - Kay Diederichs
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
| | - Wolfram Welte
- Biophysics, Fachbereich Biologie, University of Konstanz, 78457 Konstanz, Germany and
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219
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Ardèvol A, Biarnés X, Planas A, Rovira C. The Conformational Free-Energy Landscape of β-d-Mannopyranose: Evidence for a 1S5 → B2,5 → OS2 Catalytic Itinerary in β-Mannosidases. J Am Chem Soc 2010; 132:16058-65. [DOI: 10.1021/ja105520h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Albert Ardèvol
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Xevi Biarnés
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Antoni Planas
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
| | - Carme Rovira
- Computer Simulation and Modeling Laboratory and Institut de Química Teòrica i Computacional (IQTCUB), Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08018 Barcelona, Spain
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220
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Ketudat Cairns JR, Esen A. β-Glucosidases. Cell Mol Life Sci 2010; 67:3389-405. [PMID: 20490603 PMCID: PMC11115901 DOI: 10.1007/s00018-010-0399-2] [Citation(s) in RCA: 359] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 04/13/2010] [Accepted: 04/30/2010] [Indexed: 10/19/2022]
Abstract
β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.
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Affiliation(s)
- James R Ketudat Cairns
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, Thailand.
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221
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Leemhuis H, Dijkhuizen L. Engineering of Hydrolysis Reaction Specificity in the Transglycosylase Cyclodextrin Glycosyltransferase. BIOCATAL BIOTRANSFOR 2010. [DOI: 10.1080/10242420310001614333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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222
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Massa C, Guarnaccia C, Lamba D, Anselmi C. Insight into the structure of an endopolygalacturonase from the phytopathogen Burkholderia cepacia: a biochemical and computational study. Biochimie 2010; 92:1445-53. [PMID: 20637827 DOI: 10.1016/j.biochi.2010.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 07/07/2010] [Indexed: 11/30/2022]
Abstract
We have recently investigated and characterized the mode of action of BcPeh28A, an endopolygalacturonase (endoPG) from the phytopathogen Burkholderia cepacia. EndoPGs belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. Here we report a 3-D structural model of BcPeh28A by combining mass spectrometry (MS) analysis, aimed at disulphide bridges mapping, and computational modelling tools. MS analyses have revealed the complete pattern of disulphide bridges in BcPeh28A, pointing out the presence of three disulphide bonds, defined as Cys3-25, Cys216-244 and Cys309-421. A 3-D model of BcPeh28A was generated by computational methods based on profile-profile sequence alignments and fold recognition algorithms. The final model exhibits a right-handed β-helix fold with eleven β-helical coils and includes the disulphide bonds as additional spatial restraints. Molecular dynamics simulations have been performed to test the conformational stability of the model. Finally, the structural analysis of the BcPeh28A model allows defining the architecture and the amino acid topology of the subsites involved in the catalysis and in the substrate binding specificity.
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Affiliation(s)
- Claudia Massa
- Structural Biology Laboratory, Sincrotrone Trieste S.C.p.A., AREA Science Park - Basovizza Strada Statale 14, km 163,5, I-34149 Trieste, Italy.
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223
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Synthesis of 3,5-diazabicyclo [5.1.0] octenes. A new platform to mimic glycosidase transition states. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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224
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Gilbert HJ. The biochemistry and structural biology of plant cell wall deconstruction. PLANT PHYSIOLOGY 2010; 153:444-55. [PMID: 20406913 PMCID: PMC2879781 DOI: 10.1104/pp.110.156646] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 04/17/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Harry J Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA.
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225
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Kittl R, Withers SG. New approaches to enzymatic glycoside synthesis through directed evolution. Carbohydr Res 2010; 345:1272-9. [PMID: 20427037 DOI: 10.1016/j.carres.2010.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 04/02/2010] [Accepted: 04/03/2010] [Indexed: 11/26/2022]
Abstract
The expanding field of glycobiology requires tools for the synthesis of structurally defined oligosaccharides and glycoconjugates, while any potential therapeutic applications of sugar-based derivates would require access to substantial quantities of such compounds. Classical chemical approaches are not well suited for such large-scale syntheses, thus enzymatic approaches are sought. Traditional routes to the enzymatic assembly of oligosaccharides have involved the use of either Nature's own biosynthetic enzymes, the glycosyl transferases, or glycosidases run in transglycosylation mode. However, each approach has drawbacks that have limited its application. Glycosynthases are mutant glycosidases in which the catalytic nucleophile has been replaced by mutation, inactivating them as hydrolases. When used in conjunction with glycosyl fluorides of the opposite anomeric configuration to that of the substrate, these enzymes function as highly efficient transferases, frequently giving stoichiometric yields of products. Further improvements can be obtained through directed evolution of the gene encoding the enzyme in question, but this requires the ability to screen very large libraries of catalysts. In this review we survey new screening methods for the formation of glycosidic linkages using high-throughput techniques, such as FACS, chemical complementation, and robot-assisted ELISA assays. Enzymes were evolved to have higher catalytic activity with their natural substrates, to show altered substrate specificities or to be promiscuous for efficient application in oligosaccharide, glycolipid, and glycoprotein synthesis.
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Affiliation(s)
- Roman Kittl
- Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada V6T 1Z4
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226
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Jordan DB, Wagschal K. Properties and applications of microbial β-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium. Appl Microbiol Biotechnol 2010; 86:1647-58. [DOI: 10.1007/s00253-010-2538-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/02/2010] [Accepted: 03/03/2010] [Indexed: 11/28/2022]
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227
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Pollet A, Delcour JA, Courtin CM. Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families. Crit Rev Biotechnol 2010; 30:176-91. [DOI: 10.3109/07388551003645599] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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228
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Huang CL. Regulation of ion channels by secreted Klotho: mechanisms and implications. Kidney Int 2010; 77:855-60. [PMID: 20375979 DOI: 10.1038/ki.2010.73] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Klotho is an anti-aging protein predominantly expressed in the kidney, parathyroid glands, and choroid plexus of the brain. It is a single-pass transmembrane protein with a large extracellular domain. The extracellular domain of Klotho is cleaved and released into extracellular fluid, including blood, urine, and cerebrospinal fluid. The membrane-bound full-length Klotho and secreted extracellular domain of Klotho have distinct functions. Membrane Klotho interacts with fibroblast growth factor (FGF) receptors to form high-affinity receptors for FGF23. Secreted Klotho functions as a humoral factor that regulates several ion channels and transporters, and other processes, including insulin and insulin-like growth factor signaling. This mini-review focuses on the mechanisms of regulation of cell-surface abundance of ion channels by secreted Klotho and the importance of these effects of Klotho in physiology and pathological conditions.
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Affiliation(s)
- Chou-Long Huang
- Department of Medicine, UT Southwestern Medical Center, Dallas, Texas,
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229
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Schulz EC, Schwarzer D, Frank M, Stummeyer K, Mühlenhoff M, Dickmanns A, Gerardy-Schahn R, Ficner R. Structural Basis for the Recognition and Cleavage of Polysialic Acid by the Bacteriophage K1F Tailspike Protein EndoNF. J Mol Biol 2010; 397:341-51. [DOI: 10.1016/j.jmb.2010.01.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 01/11/2010] [Accepted: 01/13/2010] [Indexed: 11/16/2022]
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230
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Schulz EC, Neumann P, Gerardy-Schahn R, Sheldrick GM, Ficner R. Structure analysis of endosialidase NF at 0.98 A resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:176-80. [PMID: 20124697 DOI: 10.1107/s0907444909048720] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 11/16/2009] [Indexed: 11/10/2022]
Abstract
Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades alpha-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98 A resolution. The 210 kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid.
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Affiliation(s)
- Eike C Schulz
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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231
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Gloster TM, Davies GJ. Glycosidase inhibition: assessing mimicry of the transition state. Org Biomol Chem 2010; 8:305-20. [PMID: 20066263 PMCID: PMC2822703 DOI: 10.1039/b915870g] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/30/2009] [Indexed: 12/15/2022]
Abstract
Glycoside hydrolases, the enzymes responsible for hydrolysis of the glycosidic bond in di-, oligo- and polysaccharides, and glycoconjugates, are ubiquitous in Nature and fundamental to existence. The extreme stability of the glycosidic bond has meant these enzymes have evolved into highly proficient catalysts, with an estimated 10(17) fold rate enhancement over the uncatalysed reaction. Such rate enhancements mean that enzymes bind the substrate at the transition state with extraordinary affinity; the dissociation constant for the transition state is predicted to be 10(-22) M. Inhibition of glycoside hydrolases has widespread application in the treatment of viral infections, such as influenza and HIV, lysosomal storage disorders, cancer and diabetes. If inhibitors are designed to mimic the transition state, it should be possible to harness some of the transition state affinity, resulting in highly potent and specific drugs. Here we examine a number of glycosidase inhibitors which have been developed over the past half century, either by Nature or synthetically by man. A number of criteria have been proposed to ascertain which of these inhibitors are true transition state mimics, but these features have only be critically investigated in a very few cases.
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Affiliation(s)
- Tracey M. Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
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232
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Abstract
Despite the presence of many carbohydrolytic activities in insects, their cellulolytic mechanisms are poorly understood. Whereas cellulase genes are absent from the genomes of Drosophila melanogaster or Bombyx mori, other insects such as termites produce their own cellulases. Recent studies using molecular biological techniques have brought new insights into the mechanisms by which the insects and their microbial symbionts digest cellulose in the small intestine. DNA sequences of cellulase and associated genes, as well as physiological and morphological information about the digestive systems of cellulase-producing insects, may allow the efficient use of cellulosic biomass as a sustainable energy source.
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Affiliation(s)
- Hirofumi Watanabe
- National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki, Japan.
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233
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Nam KH, Sung MW, Hwang KY. Structural insights into the substrate recognition properties of beta-glucosidase. Biochem Biophys Res Commun 2009; 391:1131-5. [PMID: 20005197 DOI: 10.1016/j.bbrc.2009.12.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 12/08/2009] [Indexed: 11/17/2022]
Abstract
Beta-glucosidase enzymes (EC 3.2.1-3.2.3) hydrolyze sugars and are implicated in a wide spectrum of biological processes. Recently, we reported that beta-glucosidase has varied kinetic parameters for the natural and synthetic substrates [K.H Nam, S.J. Kim, M.Y. Kim, J.H. Kim, T.S. Yeo, C.M. Lee, H.K Jun, K.Y. Hwang. Crystal structure of engineered beta-glucosidase from a soil metagenome, Proteins 73 (2008) 788-793]. However, an understanding of the kinetic values of beta-glucosidase has not yet enabled the elucidation of its molecular function. Here, we report the X-ray crystal structure of beta-glucosidase with a glucose and cellobiose fragment from uncultured soil metagenome. From the various crystals, we obtained the pre-reaction (native), intermediate (disaccharide cleavage) and post-reaction (glucose binding) states of the active site pocket. These structures provide snapshots of the catalytic processing of beta-glucosidase. In addition, the intermediate state of the crystal structure provides insight into the substrate specificity of beta-glucosidase. These structural studies will facilitate elucidation of the architectural mechanism responsible for the substrate recognition of beta-glucosidase.
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Affiliation(s)
- Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, South Korea
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234
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Lagaert S, Beliën T, Volckaert G. Plant cell walls: Protecting the barrier from degradation by microbial enzymes. Semin Cell Dev Biol 2009; 20:1064-73. [DOI: 10.1016/j.semcdb.2009.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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235
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Gallardo O, Pastor FIJ, Polaina J, Diaz P, Łysek R, Vogel P, Isorna P, González B, Sanz-Aparicio J. Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution. J Biol Chem 2009; 285:2721-33. [PMID: 19940147 DOI: 10.1074/jbc.m109.064394] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.
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Affiliation(s)
- Oscar Gallardo
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
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236
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Zukerman-Schpector J, Caracelli I, Vega-Teijido M, Garcia ALL, Costenaro ER, Correia CRD. Molecular structure of two C-aryl-iminocyclitols studied by X-ray and ab initiocalculations. Z KRIST-CRYST MATER 2009. [DOI: 10.1524/zkri.220.1.45.58888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract(1), C18H26N2O7,Mr= 382.41,P212121,a= 9.7215(9),b= 10.687(1),c= 18.399(2) Å,V= 1911.6(3) Å3,Z= 4,R1= 0.0395. (2), C12H18ClNO4,Mr= 275.72,P21,a= 10.431(1),b= 6.9223(8),c= 18.043(2) Å,β= 102.085(7)°,V= 1273.9(2) Å3,Z= 4,R1= 0.0578. The five membered ring is in a twist conformation in (1) and in the two independent molecules of (2) in an envelope conformation. In both compounds the hydroxyl moieties are involved in hydrogen bonds. The compounds were studied by HF/6-31G** computations.
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237
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Gubica T, Temeriusz A, Paradowska K, Ostrowski A, Klimentowska P, Cyrański MK. Single-crystal and powder X-ray diffraction and solid-state 13C NMR of p-nitrophenyl glycopyranosides, the derivatives of d-galactose, d-glucose, and d-mannose. Carbohydr Res 2009; 344:1734-44. [DOI: 10.1016/j.carres.2009.05.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/20/2009] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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238
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Hall BG, Pikis A, Thompson J. Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations. Mol Biol Evol 2009; 26:2487-97. [PMID: 19625389 DOI: 10.1093/molbev/msp162] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Glycosyl hydrolase Family 4 (GH4) is exceptional among the 114 families in this enzyme superfamily. Members of GH4 exhibit unusual cofactor requirements for activity, and an essential cysteine residue is present at the active site. Of greatest significance is the fact that members of GH4 employ a unique catalytic mechanism for cleavage of the glycosidic bond. By phylogenetic analysis, and from available substrate specificities, we have assigned a majority of the enzymes of GH4 to five subgroups. Our classification revealed an unexpected relationship between substrate specificity and the presence, in each subgroup, of a motif of four amino acids that includes the active-site Cys residue: alpha-glucosidase, CHE(I/V); alpha-galactosidase, CHSV; alpha-glucuronidase, CHGx; 6-phospho-alpha-glucosidase, CDMP; and 6-phospho-beta-glucosidase, CN(V/I)P. The question arises: Does the presence of a particular motif sufficiently predict the catalytic function of an unassigned GH4 protein? To test this hypothesis, we have purified and characterized the alpha-glucoside-specific GH4 enzyme (PalH) from the phytopathogen, Erwinia rhapontici. The CHEI motif in this protein has been changed by site-directed mutagenesis, and the effects upon substrate specificity have been determined. The change to CHSV caused the loss of all alpha-glucosidase activity, but the mutant protein exhibited none of the anticipated alpha-galactosidase activity. The Cys-containing motif may be suggestive of enzyme specificity, but phylogenetic placement is required for confidence in that specificity. The Acholeplasma laidlawii GH4 protein is phylogenetically a phospho-beta-glucosidase but has a unique SSSP motif. Lacking the initial Cys in that motif it cannot hydrolyze glycosides by the normal GH4 mechanism because the Cys is required to position the metal ion for hydrolysis, nor can it use the more common single or double-displacement mechanism of Koshland. Several considerations suggest that the protein has acquired a new function as the consequence of positive selection. This study emphasizes the importance of automatic annotation systems that by integrating phylogenetic analysis, functional motifs, and bioinformatics data, may lead to innovative experiments that further our understanding of biological systems.
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Affiliation(s)
- Barry G Hall
- Bellingham Research Institute, Bellingham, WA, USA.
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239
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Garman SC. Structural studies on α-GAL and α-NAGAL: The atomic basis of Fabry and Schindler diseases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600598194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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240
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Trincone A, Pagnotta E, Giordano A, Perugino G, Rossi M, Moracci M. Enzymatic Synthesis of 2-Deoxyglycosides Using the ß-Glycosidase of the ArchaeonSulfolobus solfataricus. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/1024242031000076224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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241
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Kang MS, Okuyama M, Yaoi K, Mitsuishi Y, Kim YM, Mori H, Kimura A. Glycoside hydrolase family 31Escherichia coliα-xylosidase. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701806348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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242
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Yip VLY, Withers SG. Family 4 glycoside hydrolases are special: The first β-elimination mechanism amongst glycoside hydrolases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500515926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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243
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Weignerová L, Simerská P, Křen V. α-Galactosidases and their applications in biotransformations. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420802583416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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244
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Tamayo JA, Franco F, Lo Re D, Sánchez-Cantalejo F. Synthesis of Pentahydroxylated Pyrrolizidines and Indolizidines. J Org Chem 2009; 74:5679-82. [DOI: 10.1021/jo900801c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan A. Tamayo
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n 18071 Granada, Spain
| | - Francisco Franco
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n 18071 Granada, Spain
| | - Daniele Lo Re
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n 18071 Granada, Spain
| | - Fernando Sánchez-Cantalejo
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus de Cartuja, s/n 18071 Granada, Spain
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245
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Olszewska E, Borzym-Kluczyk M, Rzewnicki I, Rutkowska J, Knas M, Rogowski M, Waniewska E, Wielgosz R. Hexosaminidase as a new potential marker for larynx cancer. Clin Biochem 2009; 42:1187-9. [DOI: 10.1016/j.clinbiochem.2009.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 02/22/2009] [Accepted: 03/01/2009] [Indexed: 10/21/2022]
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246
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Vasur J, Kawai R, Andersson E, Igarashi K, Sandgren M, Samejima M, Ståhlberg J. X-ray crystal structures of Phanerochaete chrysosporium Laminarinase 16A in complex with products from lichenin and laminarin hydrolysis. FEBS J 2009; 276:3858-69. [PMID: 19769746 DOI: 10.1111/j.1742-4658.2009.07099.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The 1,3(4)-beta-D-glucanases of glycoside hydrolase family 16 provide useful examples of versatile yet specific protein-carbohydrate interactions. In the present study, we report the X-ray structures of the 1,3(4)-beta-D-glucanase Phanerochaete chrysosporium Laminarinase 16A in complex with beta-glucan products from laminarin (1.6 A) and lichenin (1.1 A) hydrolysis. The G6G3G3G glucan, in complex with the enzyme, showed a beta-1,6 branch in the acceptor site. The G4G3G ligand-protein complex showed that there was no room for a beta-1,6 branch in the -1 or -2 subsites; furthermore, the distorted residue in the -1 subsite and the glucose in the -2 subsite required a beta-1,3 bond between them. These are the first X-ray crystal structures of any 1,3(4)-beta-D-glucanase in complex with glucan products. They provide details of both substrate and product binding in support of earlier enzymatic evidence.
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Affiliation(s)
- Jonas Vasur
- Department of Molecular Biology, University of Agricultural Sciences, Uppsala, Sweden
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247
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Muzard M, Aubry N, Plantier-Royon R, O’Donohue M, Rémond C. Evaluation of the transglycosylation activities of a GH 39 β-d-xylosidase for the synthesis of xylose-based glycosides. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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248
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Petersen L, Ardèvol A, Rovira C, Reilly PJ. Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study. J Phys Chem B 2009; 113:7331-9. [DOI: 10.1021/jp811470d] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis Petersen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Albert Ardèvol
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Carme Rovira
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Peter J. Reilly
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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249
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Zhang L, Bharadwaj AG, Casper A, Barkley J, Barycki JJ, Simpson MA. Hyaluronidase activity of human Hyal1 requires active site acidic and tyrosine residues. J Biol Chem 2009; 284:9433-42. [PMID: 19201751 PMCID: PMC2666596 DOI: 10.1074/jbc.m900210200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 02/05/2009] [Indexed: 11/06/2022] Open
Abstract
Hyaluronidases are a family of endolytic glycoside hydrolases that cleave the beta1-4 linkage between N-acetylglucosamine and glucuronic acid in hyaluronan polymers via a substrate-assisted mechanism. In humans, turnover of hyaluronan by this enzyme family is critical for normal extracellular matrix remodeling. However, elevated expression of the Hyal1 isozyme accelerates tumor growth and metastatic progression. In this study, we used structural information, site-directed mutagenesis, and steady state enzyme kinetics to probe molecular determinants of human Hyal1 function. Mutagenesis of active site residues Glu(131) and Tyr(247) to Gln and Phe, respectively, eliminated activity at all hyaluronan concentrations (to 125 microm or 2.5 mg/ml). Conservative mutagenesis of Asp(129) and Tyr(202) significantly impaired catalysis by increases of 5- and 10-fold in apparent K(m) and reductions in V(max) of 95 and 50%, respectively. Tyr(247) and Asp(129) are required for stabilization of the catalytic nucleophile, which arises as a resonance intermediate of N-acetylglucosamine on the substrate. Glu(131) is a likely proton donor for the hydroxyl leaving group. Tyr(202) is a substrate binding determinant. General disulfide reduction had no effect on activity in solution, but enzymatic deglycosylation reduced Hyal1 activity in a time-dependent fashion. Mutagenesis identified Asn(350) glycosylation as the requisite modification. Deletion of the C-terminal epidermal growth factor-like domain, in which Asn(350) is located, also eliminated activity, irrespective of glycosylation. Collectively, these studies define key components of Hyal1 active site catalysis, and structural factors critical for stability. Such detailed understanding will allow rational design of enzyme modulators.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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250
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Hurtado-Guerrero R, Schüttelkopf AW, Mouyna I, Ibrahim AFM, Shepherd S, Fontaine T, Latgé JP, van Aalten DMF. Molecular mechanisms of yeast cell wall glucan remodeling. J Biol Chem 2009; 284:8461-9. [PMID: 19097997 PMCID: PMC2659204 DOI: 10.1074/jbc.m807990200] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 12/19/2008] [Indexed: 11/06/2022] Open
Abstract
Yeast cell wall remodeling is controlled by the equilibrium between glycoside hydrolases, glycosyltransferases, and transglycosylases. Family 72 glycoside hydrolases (GH72) are ubiquitous in fungal organisms and are known to possess significant transglycosylase activity, producing elongated beta(1-3) glucan chains. However, the molecular mechanisms that control the balance between hydrolysis and transglycosylation in these enzymes are not understood. Here we present the first crystal structure of a glucan transglycosylase, Saccharomyces cerevisiae Gas2 (ScGas2), revealing a multidomain fold, with a (betaalpha)(8) catalytic core and a separate glucan binding domain with an elongated, conserved glucan binding groove. Structures of ScGas2 complexes with different beta-glucan substrate/product oligosaccharides provide "snapshots" of substrate binding and hydrolysis/transglycosylation giving the first insights into the mechanisms these enzymes employ to drive beta(1-3) glucan elongation. Together with mutagenesis and analysis of reaction products, the structures suggest a "base occlusion" mechanism through which these enzymes protect the covalent protein-enzyme intermediate from a water nucleophile, thus controlling the balance between hydrolysis and transglycosylation and driving the elongation of beta(1-3) glucan chains in the yeast cell wall.
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Affiliation(s)
- Ramon Hurtado-Guerrero
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
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