251
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Shanmugasundaram B, Vasella A. Synthesis of NewC(2)-Substitutedgluco-Configured Tetrahydroimidazopyridines and Their Evaluation as Glucosidase Inhibitors. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590199] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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252
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A new route into hexahydro-cyclopenta[b]pyrrole-cis-3a,6-diols. Synthesis of constrained bicyclic analogues of pyrrolidine azasugars. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.08.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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253
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Taylor EJ, Goyal A, Guerreiro CIPD, Prates JAM, Money VA, Ferry N, Morland C, Planas A, Macdonald JA, Stick RV, Gilbert HJ, Fontes CMGA, Davies GJ. How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides. J Biol Chem 2005; 280:32761-7. [PMID: 15987675 DOI: 10.1074/jbc.m506580200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the most intriguing features of the 90 glycoside hydrolase families (GHs) is the range of specificities displayed by different members of the same family, whereas the catalytic apparatus and mechanism are often invariant. Family GH26 predominantly comprises beta-1,4 mannanases; however, a bifunctional Clostridium thermocellum GH26 member (hereafter CtLic26A) displays a markedly different specificity. We show that CtLic26A is a lichenase, specific for mixed (Glcbeta1,4Glcbeta1,4Glcbeta1,3)n oligo- and polysaccharides, and displays no activity on manno-configured substrates or beta-1,4-linked homopolymers of glucose or xylose. The three-dimensional structure of the native form of CtLic26A has been solved at 1.50-A resolution, revealing a characteristic (beta/alpha)8 barrel with Glu-109 and Glu-222 acting as the catalytic acid/base and nucleophile in a double-displacement mechanism. The complex with the competitive inhibitor, Glc-beta-1,3-isofagomine (Ki 1 microm), at 1.60 A sheds light on substrate recognition in the -2 and -1 subsites and illuminates why the enzyme is specific for lichenan-based substrates. Hydrolysis of beta-mannosides by GH26 members is thought to proceed through transition states in the B2,5 (boat) conformation in which structural distinction of glucosides versus mannosides reflects not the configuration at C2 but the recognition of the pseudoaxial O3 of the B2,5 conformation. We suggest a different conformational itinerary for the GH26 enzymes active on gluco-configured substrates.
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Affiliation(s)
- Edward J Taylor
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5YW, United Kingdom
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254
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255
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Simons JP, Jockusch RA, ÇarÇabal P, Hünig I, Kroemer RT, Macleod NA, Snoek LC. Sugars in the gas phase. Spectroscopy, conformation, hydration, co-operativity and selectivity. INT REV PHYS CHEM 2005. [DOI: 10.1080/01442350500415107] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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256
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Maurus R, Begum A, Kuo HH, Racaza A, Numao S, Andersen C, Tams JW, Vind J, Overall CM, Withers SG, Brayer GD. Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase. Protein Sci 2005; 14:743-55. [PMID: 15722449 PMCID: PMC2279296 DOI: 10.1110/ps.041079305] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mechanism of allosteric activation of alpha-amylase by chloride has been studied through structural and kinetic experiments focusing on the chloride-dependent N298S variant of human pancreatic alpha-amylase (HPA) and a chloride-independent TAKA-amylase. Kinetic analysis of the HPA variant clearly demonstrates the pronounced activating effect of chloride ion binding on reaction rates and its effect on the pH-dependence of catalysis. Structural alterations observed in the N298S variant upon chloride ion binding suggest that the chloride ion plays a variety of roles that serve to promote catalysis. One of these is having a strong influence on the positioning of the acid/base catalyst residue E233. Absence of chloride ion results in multiple conformations for this residue and unexpected enzymatic products. Chloride ion and N298 also appear to stabilize a helical region of polypeptide chain from which projects the flexible substrate binding loop unique to chloride-dependent alpha-amylases. This structural feature also serves to properly orient the catalytically essential residue D300. Comparative analyses show that the chloride-independent alpha-amylases compensate for the absence of bound chloride by substituting a hydrophobic core, altering the manner in which substrate interactions are made and shifting the placement of N298. These evolutionary differences presumably arise in response to alternative operating environments or the advantage gained in a particular product profile. Attempts to engineer chloride-dependence into the chloride-independent TAKA-amylase point out the complexity of this system, and the fact that a multitude of factors play a role in binding chloride ion in the chloride-dependent alpha-amylases.
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Affiliation(s)
- Robert Maurus
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
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257
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Westermann B, Neuhaus C. Dihydroxyaceton in Aminosäure-katalysierten Mannich-Reaktionen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500297] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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258
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Westermann B, Neuhaus C. Dihydroxyacetone in Amino Acid Catalyzed Mannich-Type Reactions. Angew Chem Int Ed Engl 2005; 44:4077-9. [PMID: 15912549 DOI: 10.1002/anie.200500297] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bernhard Westermann
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, 06 120 Halle (Saale), Germany.
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259
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Dookhun V, Bennet AJ. Unexpected Stability of Aryl β-N-Acetylneuraminides in Neutral Solution: Biological Implications for Sialyl Transfer Reactions. J Am Chem Soc 2005; 127:7458-65. [PMID: 15898795 DOI: 10.1021/ja042280e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A reagent panel comprised of seven aryl beta-D-N-acetylneuraminides was synthesized and then used to probe the mechanisms of nonenzymatic hydrolysis. These reactions proceeded via four independent pathways: (1) acid-catalyzed hydrolysis of the neutral molecule; (2) acid-catalyzed hydrolysis of the anionic form, or its kinetic equivalent spontaneous hydrolysis of the neutral form; (3) spontaneous hydrolysis of the anionic form; and (4) a base-promoted pathway. The pH-independent spontaneous hydrolysis of 4-nitrophenyl alpha-D-N-acetylneuraminide (5) occurs at a rate that is over 100 times faster than that of the corresponding reaction of 4-nitrophenyl beta-D-N-acetylneuraminide (4a). Spontaneous hydrolyses of four aryl beta-D-N-acetylneuraminides displayed a beta(lg) value of -1.24 +/- 0.16 (pH = 8.1, T = 100 degrees C), and at a pH value of 1.0 (50 degrees C), all seven panel members gave a beta(lg) value of 0.14 +/- 0.08. The aqueous ethanolyses of 4a and 5 gave similar products and displayed sensitivity parameters (m) in a standard Winstein-Grunwald analysis of -0.04 +/- 0.01 and +0.23 +/- 0.02, respectively. These results, plus the activation parameters calculated for the spontaneous hydrolyses of the anionic forms of 5 (DeltaH() = 116 +/- 2 kJ mol(-1) and DeltaS = 27 +/- 4 J mol(-1) K(-1)) and 4a (DeltaH = 138 +/- 3 kJ mol(-1) and DeltaS = 59 +/- 8 J mol(-1) K(-1)), are inconsistent with anomeric carboxylate assistance occurring during the hydrolysis reactions, and the likely cause for the enhanced reactivity of 5 in comparison to that of 4a is an increase in ground-state steric strain.
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Affiliation(s)
- Veedeeta Dookhun
- Department of Chemistry, Simon Fraser University, Burnaby, B.C., Canada
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260
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Synthesis of d-gluco-, l-ido-, d-galacto-, and l-altro-configured glycaro-1,5-lactams from tartaric acid. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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261
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Hancock SM, Corbett K, Fordham-Skelton AP, Gatehouse JA, Davis BG. Developing Promiscuous Glycosidases for Glycoside Synthesis: Residues W433 and E432 in Sulfolobus solfataricus β-Glycosidase are Important Glucoside- and Galactoside-Specificity Determinants. Chembiochem 2005; 6:866-75. [PMID: 15846595 DOI: 10.1002/cbic.200400341] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two residues that have been implicated in determining the substrate specificity of the thermophilic beta-glycosidase from the archaeon Sulfolobus solfataricus (SsbetaG), a member of the glycosyl hydrolase family 1, have been mutated by site-directed mutagenesis so as to create more versatile catalysts for carbohydrate chemistry. The wild-type and mutated sequences were expressed in E. coli with a His(7)-tag to allow one-step chromatographic purification. The E432C and W433C mutations removed key interactions with the OH-4 and OH-3 of the sugar substrates, thus reducing the discrimination of glucose, galactose and fucose with respect to other glycosides. This resulted in two glycosidases with greatly broadened substrate specificities. Observed changes include a 24-fold increase in Man:Gal activity and an 18-fold increase in GalA:Gal activity. This promiscuous substrate tolerance was further illustrated by the parallel synthesis of a beta-glycoside library of glucose, galactose, xylose and mannose in one pot at 50 degrees C, in organic solvent. The synthetic potential of the catalysts was further evaluated through alkyl glycoside transglycosylation yields, including the first examples of synthesis of beta-mannosides and beta-xylosides with SsbetaG.
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Affiliation(s)
- Susan M Hancock
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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262
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Watson JN, Newstead S, Dookhun V, Taylor G, Bennet AJ. Contribution of the active site aspartic acid to catalysis in the bacterial neuraminidase from Micromonospora viridifaciens. FEBS Lett 2005; 577:265-9. [PMID: 15527797 DOI: 10.1016/j.febslet.2004.10.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 09/30/2004] [Accepted: 10/06/2004] [Indexed: 11/20/2022]
Abstract
A recombinant D92G mutant sialidase from Micromonospora viridifaciens has been cloned, expressed and purified. Kinetic studies reveal that the replacement of the conserved aspartic acid with glycine results in a catalytically competent retaining sialidase that possesses significant activity against activated substrates. The contribution of this aspartate residue to the free energy of hydrolysis for natural substrates is greater than 19 kJ/mol. The three dimensional structure of the D92G mutant shows that the removal of aspartic acid 92 causes no significant re-arrangement of the active site, and that an ordered water molecule substitutes for the carboxylate group of D92.
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Affiliation(s)
- Jacqueline N Watson
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
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263
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Li H, Blériot Y, Mallet JM, Rodriguez-Garcia E, Vogel P, Zhang Y, Sinaÿ P. New 1-amino-1-deoxy- and 2-amino-2-deoxy-polyhydroxyazepanes: synthesis and inhibition of glycosidases. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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264
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Cox LR, DeBoos GA, Fullbrook JJ, Percy JM, Spencer N. Applying asymmetric dihydroxylation to the synthesis of difluorinated carbohydrate analogues: a 1,1-difluoro-1-deoxy-d-xylulose. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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265
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Nerinckx W, Desmet T, Piens K, Claeyssens M. An elaboration on thesyn-antiproton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy. FEBS Lett 2004; 579:302-12. [PMID: 15642336 DOI: 10.1016/j.febslet.2004.12.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 12/10/2004] [Accepted: 12/10/2004] [Indexed: 11/16/2022]
Abstract
An in silico survey of all known 3D-structures of glycoside hydrolases that contain a ligand in the -1 subsite is presented. A recurrent crucial positioning of active site residues indicates a common general strategy for electrostatic stabilisation directed to the carbohydrate's ring-oxygen at the transition state. This is substantially different depending on whether the enzyme's proton donor is syn or anti positioned versus the substrate. A comprehensive list of enzymes belonging to 42 different families is given and selected examples are described. An implication for an early evolution scenario of glycoside hydrolases is discussed.
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Affiliation(s)
- W Nerinckx
- Laboratory for Glycobiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.
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266
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Godin G, Compain P, Martin OR, Ikeda K, Yu L, Asano N. α-1-C-Alkyl-1-deoxynojirimycin derivatives as potent and selective inhibitors of intestinal isomaltase: remarkable effect of the alkyl chain length on glycosidase inhibitory profile. Bioorg Med Chem Lett 2004; 14:5991-5. [PMID: 15546715 DOI: 10.1016/j.bmcl.2004.09.086] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 09/30/2004] [Accepted: 09/30/2004] [Indexed: 11/20/2022]
Abstract
A series of alpha- and beta-1-C-alkyl-1-deoxynojirimycin derivatives was prepared and evaluated as glycosidase inhibitors. Biological assays showed a marked dependence of the selectivity and potency of the inhibitors upon the position of the alkyl chain (alpha-1-C-, beta-1-C- or N-alkyl derivatives). In addition, the efficiency of alpha-1-C-alkyl-1-deoxynojirimycin derivatives as intestinal isomaltase inhibitors increases with the length of the alkyl chain. The strongest inhibition was found for alpha-1-C -nonyl-1-deoxynojirimycin with an IC50=3.5 nM (25x more potent inhibitor than the shorter chain homologue carrying a C8 chain). These results demonstrate that subtle changes in the aglycon fragment may result in remarkable enzyme specificity.
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Affiliation(s)
- Guillaume Godin
- Institut de Chimie Organique et Analytique, Université d'Orléans, CNRS UMR 6005, BP 6759, 45067 Orléans, France
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267
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Terinek M, Vasella A. Synthesis of Tetrahydropyridoimidazole-2-acetates: Effect of Carboxy and Methoxycarbonyl Groups at C(2) on the Inhibition of Some?- and?-Glycosidases. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490273] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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268
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Gloster TM, Macdonald JM, Tarling CA, Stick RV, Withers SG, Davies GJ. Structural, Thermodynamic, and Kinetic Analyses of Tetrahydrooxazine-derived Inhibitors Bound to β-Glucosidases. J Biol Chem 2004; 279:49236-42. [PMID: 15356002 DOI: 10.1074/jbc.m407195200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The understanding of transition state mimicry in glycoside hydrolysis is increasingly important both in the quest for novel specific therapeutic agents and for the deduction of enzyme function and mechanism. To aid comprehension, inhibitors can be characterized through kinetic, thermodynamic, and structural dissection to build an "inhibition profile." Here we dissect the binding of a tetrahydrooxazine inhibitor and its derivatives, which display Ki values around 500 nm. X-ray structures with both a beta-glucosidase, at 2 A resolution, and an endoglucanase at atomic (approximately 1 A) resolution reveal similar interactions between the tetrahydrooxazine inhibitor and both enzymes. Kinetic analyses reveal the pH dependence of kcat/Km and 1/Ki with both enzyme systems, and isothermal titration calorimetry unveils the enthalpic and entropic contributions to beta-glucosidase inhibition. The pH dependence of enzyme activity mirrored that of 1/Ki in both enzymes, unlike the cases of isofagomine and 1-deoxynojirimycin that have been characterized previously. Calorimetric dissection reveals a large favorable enthalpy that is partially offset by an unfavorable entropy upon binding. In terms of the similar profile for the pH dependence of 1/Ki and the pH dependence of kcat/Km, the significant enthalpy of binding when compared with other glycosidase inhibitors, and the tight binding at the optimal pH of the enzymes tested, tetrahydrooxazine and its derivatives are a significantly better class of glycosidase inhibitor than previously assumed.
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Affiliation(s)
- Tracey M Gloster
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
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269
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Vincent F, Gloster TM, Macdonald J, Morland C, Stick RV, Dias FMV, Prates JAM, Fontes CMGA, Gilbert HJ, Davies GJ. Common Inhibition of Both β-Glucosidases and β-Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis. Chembiochem 2004; 5:1596-9. [PMID: 15515081 DOI: 10.1002/cbic.200400169] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Florence Vincent
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK
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270
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Böhm M, Vasella A. Probing the Conformational Changes in the Enzymatic Hydrolysis of 2-Acetamido-2-deoxy-β-D-glucopyranosides. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490229] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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271
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Li B, Kawatkar SP, George S, Strachan H, Woods RJ, Siriwardena A, Moremen KW, Boons GJ. Inhibition of Golgi Mannosidase II with Mannostatin A Analogues: Synthesis, Biological Evaluation, and Structure-Activity Relationship Studies. Chembiochem 2004; 5:1220-7. [PMID: 15368573 DOI: 10.1002/cbic.200300842] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mannostatin and aminocyclopentitetrol analogues with various substitutions at the amino function were synthesized. These compounds were tested as inhibitors of human Golgi and lysosomal alpha-mannosidases. Modification of the amine of mannostatin had only marginal effects, whereas similar modifications of aminocyclopentitetrol led to significantly improved inhibitors. Ab initio calculations and molecular docking studies were employed to rationalize the results. It was found that mannostatin and aminocyclopentitretrol could bind to Golgi alpha-mannosidase II in a similar mode to that of the known inhibitor swainsonine. However, due to the flexibility of the five-membered rings of these compounds, additional low-energy binding modes could be adopted. These binding modes may be relevant for the improved activities of the benzyl-substituted compounds. The thiomethyl moiety of mannostatin was predicted to make favorable hydrophobic interactions with Arg228 and Tyr727 that would possibly account for its greater inhibitory activity.
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Affiliation(s)
- Bing Li
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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272
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El Blidi L, Crestia D, Gallienne E, Demuynck C, Bolte J, Lemaire M. A straightforward synthesis of an aminocyclitol based on an enzymatic aldol reaction and a highly stereoselective intramolecular Henry reaction. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.06.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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273
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Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, Fushinobu S. Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure 2004; 12:937-47. [PMID: 15274915 DOI: 10.1016/j.str.2004.03.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 03/08/2004] [Accepted: 03/09/2004] [Indexed: 10/26/2022]
Abstract
Vibrio proteolyticus chitobiose phosphorylase (ChBP) belongs to glycosyl transferase family 36 (GT-36), and catalyzes the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. As the first known structures of a GT-36 enzyme, we determined the crystal structure of ChBP in a ternary complex with GlcNAc and SO(4). It is also the first structures of an inverting phosphorolytic enzyme in a complex with a sugar and a sulfate ion, and reveals a pseudo-ternary complex structure of enzyme-sugar-phosphate. ChBP comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain, constituting a distinctive structure among GT families. Instead, it shows significant structural similarity with glycoside hydrolase (GH) enzymes, glucoamylases (GH-15), and maltose phosphorylase (GH-65) in clan GH-L. The structural similarity reported here, together with distant sequence similarities between ChBP and GHs, led to the reclassification of family GT-36 into a novel GH family, namely GH-94.
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Affiliation(s)
- Masafumi Hidaka
- Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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274
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Blériot Y, Vadivel SK, Herrera AJ, Greig IR, Kirby AJ, Sinaÿ P. Synthesis and acid catalyzed hydrolysis of B2,5 type conformationally constrained glucopyranosides: incorporation into a cellobiose analogue. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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275
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Verdoucq L, Morinière J, Bevan DR, Esen A, Vasella A, Henrissat B, Czjze M. Structural Determinants of Substrate Specificity in Family 1 β-Glucosidases. J Biol Chem 2004; 279:31796-803. [PMID: 15148317 DOI: 10.1074/jbc.m402918200] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant beta-glucosidases play a crucial role in defense against pests. They cleave, with variable specificity, beta-glucosides to release toxic aglycone moieties. The Sorghum bicolor beta-glucosidase isoenzyme Dhr1 has a strict specificity for its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-D-glucoside), whereas its close homolog, the maize beta-glucosidase isoenzyme Glu1, which shares 72% sequence identity, hydrolyzes a broad spectrum of substrates in addition to its natural substrate 2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one. Structural data from enzyme.substrate complexes of Dhr1 show that the mode of aglycone binding differs from that previously observed in the homologous maize enzyme. Specifically, the data suggest that Asn(259), Phe(261), and Ser(462), located in the aglycone-binding site of S. bicolor Dhr1, are crucial for aglycone recognition and binding. The tight binding of the aglycone moiety of dhurrin promotes the stabilization of the reaction intermediate in which the glycone moiety is in a deformed (1)S(3) conformation within the glycone-binding site, ready for nucleophilic attack to occur. Compared with the broad specificity maize beta-glucosidase, this different binding mode explains the narrow specificity of sorghum dhurrinase-1.
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Affiliation(s)
- Lionel Verdoucq
- Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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276
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Garman SC, Garboczi DN. The molecular defect leading to Fabry disease: structure of human alpha-galactosidase. J Mol Biol 2004; 337:319-35. [PMID: 15003450 DOI: 10.1016/j.jmb.2004.01.035] [Citation(s) in RCA: 284] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 01/16/2004] [Accepted: 01/21/2004] [Indexed: 01/01/2023]
Abstract
Fabry disease is an X-linked lysosomal storage disease afflicting 1 in 40,000 males with chronic pain, vascular degeneration, cardiac impairment, and other symptoms. Deficiency in the lysosomal enzyme alpha-galactosidase (alpha-GAL) causes an accumulation of its substrate, which ultimately leads to Fabry disease symptoms. Here, we present the structure of the human alpha-GAL glycoprotein determined by X-ray crystallography. The structure is a homodimer with each monomer containing a (beta/alpha)8 domain with the active site and an antiparallel beta domain. N-linked carbohydrate appears at six sites in the glycoprotein dimer, revealing the basis for lysosomal transport via the mannose-6-phosphate receptor. To understand how the enzyme cleaves galactose from glycoproteins and glycolipids, we also determined the structure of the complex of alpha-GAL with its catalytic product. The catalytic mechanism of the enzyme is revealed by the location of two aspartic acid residues (D170 and D231), which act as a nucleophile and an acid/base, respectively. As a point mutation in alpha-GAL can lead to Fabry disease, we have catalogued and plotted the locations of 245 missense and nonsense mutations in the three-dimensional structure. The structure of human alpha-GAL brings Fabry disease into the realm of molecular diseases, where insights into the structural basis of the disease phenotypes might help guide the clinical treatment of patients.
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Affiliation(s)
- Scott C Garman
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Twinbrook II, 12441 Parklawn Drive, Rockville, MD 20852, USA.
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277
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Alberto F, Bignon C, Sulzenbacher G, Henrissat B, Czjzek M. The Three-dimensional Structure of Invertase (β-Fructosidase) from Thermotoga maritima Reveals a Bimodular Arrangement and an Evolutionary Relationship between Retaining and Inverting Glycosidases. J Biol Chem 2004; 279:18903-10. [PMID: 14973124 DOI: 10.1074/jbc.m313911200] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thermotoga maritima invertase (beta-fructosidase) hydrolyzes sucrose to release fructose and glucose, which are major carbon and energy sources for both prokaryotes and eukaryotes. The name "invertase" was given to this enzyme over a century ago, because the 1:1 mixture of glucose and fructose that it produces was named "invert sugar." Despite its name, the enzyme operates with a mechanism leading to the retention of the anomeric configuration at the site of cleavage. The enzyme belongs to family GH32 of the sequence-based classification of glycosidases. The crystal structure, determined at 2-A resolution, reveals two modules, namely a five-bladed beta-propeller with structural similarity to the beta-propeller structures of glycosidase from families GH43 and GH68 connected to a beta-sandwich module. Three carboxylates at the bottom of a deep, negatively charged funnel-shaped depression of the beta-propeller are essential for catalysis and function as nucleophile, general acid, and transition state stabilizer, respectively. The catalytic machinery of invertase is perfectly superimposable to that of the enzymes of families GH43 and GH68. The variation in the position of the furanose ring at the site of cleavage explains the different mechanisms evident in families GH32 and GH68 (retaining) and GH43 (inverting) furanosidases.
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Affiliation(s)
- François Alberto
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Université Aix-Marseille I & II, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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278
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Lee JK, Bain AD, Berti PJ. Probing the Transition States of Four Glucoside Hydrolyses with13C Kinetic Isotope Effects Measured at Natural Abundance by NMR Spectroscopy. J Am Chem Soc 2004; 126:3769-76. [PMID: 15038730 DOI: 10.1021/ja0394028] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic isotope effects (KIEs) were measured for methyl glucoside (4) hydrolysis on unlabeled material by NMR. Twenty-eight (13)C KIEs were measured on the acid-catalyzed hydrolysis of alpha-4 and beta-4, as well as enzymatic hydrolyses with yeast alpha-glucosidase and almond beta-glucosidase. The 1-(13)C KIEs on the acid-catalyzed reactions of alpha-4 and beta-4, 1.007(2) and 1.010(6), respectively, were in excellent agreement with the previously reported values (1.007(1), 1.011(2): Bennet and Sinnott, J. Am. Chem. Soc. 1986, 108, 7287). Transition state analysis of the acid-catalyzed reactions using the (13)C KIEs, along with the previously reported (2)H KIEs, confirmed that both reactions proceed with a stepwise D(N)A(N) mechanism and showed that the glucosyl oxocarbenium ion intermediate exists in an E(3) sofa or (4)H(3) half-chair conformation. (13)C KIEs showed that the alpha-glucosidase reaction also proceeded through a D(N)*A(N) mechanism, with a 1-(13)C KIE of 1.010(4). The secondary (13)C KIEs showed evidence of distortions in the glucosyl ring at the transition state. For the beta-glucosidase-catalyzed reaction, the 1-(13)C KIE of 1.032(1) demonstrated a concerted A(N)D(N) mechanism. The pattern of secondary (13)C KIEs was similar to the acid-catalyzed reaction, showing no signs of distortion. KIE measurement at natural abundance makes it possible to determine KIEs much more quickly than previously, both by increasing the speed of KIE measurement and by obviating the need for synthesis of isotopically labeled compounds.
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Affiliation(s)
- Jason K Lee
- Department of Chemistry, Antimicrobial Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada
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279
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Hrmova M, De Gori R, Smith BJ, Vasella A, Varghese JN, Fincher GB. Three-dimensional Structure of the Barley β-d-Glucan Glucohydrolase in Complex with a Transition State Mimic. J Biol Chem 2004; 279:4970-80. [PMID: 14597633 DOI: 10.1074/jbc.m307188200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glucophenylimidazole (PheGlcIm), a tetrahydroimidazopyridine-type inhibitor and 4H3 conformer mimic of a glucoside, binds very tightly to a barley beta-d-glucan glucohydrolase, with a Ki constant of 2 x 10(-9) m and a DeltaG of 51 kJ mol(-1). PheGlcIm binds to the barley beta-d-glucan glucohydrolase approximately 2 x 10(5) times tighter than laminarin, which is the best non-synthetic ground-state substrate found so far for this enzyme, 10(6) times tighter than 4-nitrophenyl beta-d-glucopyranoside, and 2 x 10(7) tighter than glucose. The three-dimensional structure of the beta-d-glucan glucohydrolase with bound PheGlcIm indicates that the complex resembles a hypothetical transition state during the hydrolytic cycle, that the enzyme derives substrate binding energy from the "aglycone" portion of the ligand, and that it also reveals an anti-protonation trajectory for hydrolysis. Continuous electron densities at the 1.6 sigma level form between the three active site residues Asp95, His207, and Asp285, and the C6OH, C7OH, C8OH, and C9OH groups of PheGlcIm. These electron densities correspond to the most favorable interactions in the three-dimensional structure of the beta-d-glucan glucohydrolase-PheGlcIm complex and indicate atomic distances equal to or less than 2.55 A. The crystallographic data were corroborated with ab initio molecular orbital calculations. The data indicate that the 4E conformation of the glucose part of PheGlcIm is critical for tight binding and provide the first evidence for probable substrate distortion during catalysis by this enzyme.
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Affiliation(s)
- Maria Hrmova
- Faculty of Sciences, School of Agriculture and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia.
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280
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Heck MP, Vincent SP, Murray BW, Bellamy F, Wong CH, Mioskowski C. Cyclic Amidine Sugars as Transition-State Analogue Inhibitors of Glycosidases: Potent Competitive Inhibitors of Mannosidases. J Am Chem Soc 2004; 126:1971-9. [PMID: 14971930 DOI: 10.1021/ja037822r] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of monocyclic glycoamidines bearing different exocyclic amine, alcohol, or alkyl functionalities and bicyclic amidines derived from D-glucose and D-mannose were synthesized and tested as inhibitors of various glycosidases. All the prepared compounds demonstrated good to excellent inhibition toward glycosidases. In particular, the biscationic D-mannoamidine 9b bearing an exocyclic ethylamine moiety proved to be a selective competitive inhibitor of alpha- and beta-mannosidases (K(i) = 6 nM) making it the most potent inhibitor of these glycosidases reported to date. A favorable B(2,5) boat conformation might explain the selectivity of mannosidase inhibition compared to other glycosidases.
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Affiliation(s)
- Marie-Pierre Heck
- CEA, CE-Saclay, Service de Marquage Moléculaire et de Chimie Bioorganique, Bât 547, Département de Biologie Joliot-Curie, 91191 Gif Sur Yvette, France.
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281
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Kankainen M, Laitinen T, Peräkylä M. Recognition of reactive high-energy conformations by shape complementarity and specific enzyme–substrate interactions in family 10 and 11 xylanases. Phys Chem Chem Phys 2004. [DOI: 10.1039/b409589h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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282
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Li H, Blériot Y, Chantereau C, Mallet JM, Sollogoub M, Zhang Y, Rodríguez-García E, Vogel P, Jiménez-Barbero J, Sinaÿ P. The first synthesis of substituted azepanes mimicking monosaccharides: a new class of potent glycosidase inhibitors. Org Biomol Chem 2004; 2:1492-9. [PMID: 15136805 DOI: 10.1039/b402542c] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of the first examples of seven-membered ring iminoalditols, molecules displaying an extra hydroxymethyl substituent on their seven-membered ring compared to the previously reported polyhydroxylated azepanes, has been achieved from d-arabinose in 10 steps using RCM of a protected N-allyl-aminohexenitol as a key step. While the (2R,3R,4R)-2-hydroxymethyl-3,4-dihydroxy-azepane 10, a seven-membered ring analogue of fagomine, is a weak inhibitor of glycosidases, the (2R,3R,4R,5S,6S)-2-hydroxymethyl-3,4,5,6-tetrahydroxy-azepane 9 selectively inhibits green coffee bean alpha-galactosidase in the low micromolar range (Ki = 2.2 muM) despite a D-gluco relative configuration.
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Affiliation(s)
- Hongqing Li
- Ecole Normale Supérieure, Département de Chimie, UMR 8642, 24 rue Lhomond, 75231 Paris 05, France
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283
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Ferchichi M, Rémond C, Simo R, O'Donohue MJ. Investigation of the functional relevance of the catalytically important Glu(28) in family 51 arabinosidases. FEBS Lett 2003; 553:381-6. [PMID: 14572655 DOI: 10.1016/s0014-5793(03)01061-5] [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: 11/27/2022]
Abstract
The alpha-L-arabinofuranosidase (AbfD3) from Thermobacillus xylanilyticus is a family 51 glycosyl hydrolase. According to classification hierarchy, family 51 belongs to clan GH-A. While the major GH-A motifs, the catalytic acid-base and nucleophile, are conserved in AbfD3, a third catalytically important residue (Glu(28)) does not appear to be analogous to any known GH-A motif. To evaluate the importance of Glu(28), bioinformatics analyses and site-saturation mutagenesis were performed. The results indicate that Glu(28) forms part of a family 51 arabinosidase motif which might be functionally homologous to a conserved N-terminal motif found in exo-acting enzymes from families 1 and 5. Importantly, the data reveal that Glu(28) is a key determinant of substrate recognition in the -1 subsite, where it may also play an important role in water-mediated deglycosylation of the glycosyl-enzyme covalent intermediate.
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Affiliation(s)
- Mounir Ferchichi
- Institut National de la Recherche Agronomique, UMR FARE, 8, rue Gabriel Voisin, P.O. Box 316, 51688 Cedex 2 Reims, France
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284
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Numao S, Kuntz DA, Withers SG, Rose DR. Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. J Biol Chem 2003; 278:48074-83. [PMID: 12960159 DOI: 10.1074/jbc.m309249200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The family 38 golgi alpha-mannosidase II, thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate, is a clinically important enzyme involved in glycoprotein processing. The structure of three different covalent glycosyl-enzyme intermediates have been determined to 1.2-A resolution for the Golgi alpha-mannosidase II from Drosophila melanogaster by use of fluorinated sugar analogues, both with the wild-type enzyme and a mutant enzyme in which the acid/base catalyst has been removed. All these structures reveal sugar intermediates bound in a distorted 1S5 skew boat conformation. The similarity of this conformation with that of the substrate in the recently determined structure of the Michaelis complex of a beta-mannanase (Ducros, V. M. A., Zechel, D. L., Murshudov, G. N., Gilbert, H. J., Szabo, L., Stoll, D., Withers, S. G., and Davies, G. J. (2002) Angew. Chem. Int. Ed. Engl. 41, 2824-2827) suggests that these disparate enzymes have recruited common stereoelectronic features in evolving their catalytic mechanisms.
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Affiliation(s)
- Shin Numao
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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285
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Golan G, Shallom D, Teplitsky A, Zaide G, Shulami S, Baasov T, Stojanoff V, Thompson A, Shoham Y, Shoham G. Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J Biol Chem 2003; 279:3014-24. [PMID: 14573597 DOI: 10.1074/jbc.m310098200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism. Here we describe several high resolution crystal structures of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in complex with its substrate and products. In the complex of AguA with the intact substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a half-chair conformation, which is closer to the planar conformation required for the oxocarbenium ion-like transition state structure. In the active site, a water molecule is coordinated between two carboxylic acids, in an appropriate position to act as a nucleophile. From the structural data it is likely that two carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic water molecule. The loop carrying the catalytic general acid Glu(285) cannot be resolved in some of the structures but could be visualized in its "open" and "closed" (catalytic) conformations in other structures. The protonated state of Glu(285) is presumably stabilized by its proximity to the negative charge of the substrate, representing a new variation of substrate-assisted catalysis mechanism.
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Affiliation(s)
- Gali Golan
- Department of Inorganic Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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286
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Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D. Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J 2003; 22:4922-32. [PMID: 14517232 PMCID: PMC204477 DOI: 10.1093/emboj/cdg494] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
High-resolution crystal structures of alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (beta/alpha)8-barrel and a 12-stranded beta sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl-enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 A apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein-substrate interactions. The enzyme is an anti-protonator, and a 1.7 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.
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Affiliation(s)
- Klaus Hövel
- Institute for Biochemistry, University of Cologne, Cologne 50674, Germany
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287
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Meng G, Fütterer K. Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Mol Biol 2003; 10:935-41. [PMID: 14517548 DOI: 10.1038/nsb974] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2003] [Accepted: 07/31/2003] [Indexed: 11/09/2022]
Abstract
Many bacteria and about 40,000 plant species form primary carbohydrate reserves based on fructan; these polymers of beta-D-fructofuranose are thought to confer tolerance to drought and frost in plants. Microbial fructan, the beta(2,6)-linked levan, is synthesized directly from sucrose by levansucrase, which is able to catalyze both sucrose hydrolysis and levan polymerization. The crystal structure of Bacillus subtilis levansucrase, determined to a resolution of 1.5 A, shows a rare five-fold beta-propeller topology with a deep, negatively charged central pocket. Arg360, a residue essential for polymerase activity, lies in a solvent-exposed site adjacent to the central pocket. Mutagenesis data and the sucrose-bound structure of inactive levansucrase E342A, at a resolution of 2.1 A, strongly suggest that three conserved acidic side chains in the central pocket are critical for catalysis, and presumably function as nucleophile (Asp86) and general acid (Glu342), or stabilize the transition state (Asp247).
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Affiliation(s)
- Guoyu Meng
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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288
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289
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Stivers JT, Jiang YL. A mechanistic perspective on the chemistry of DNA repair glycosylases. Chem Rev 2003; 103:2729-59. [PMID: 12848584 DOI: 10.1021/cr010219b] [Citation(s) in RCA: 377] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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290
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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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291
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Abstract
Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature. These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research. During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.
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Affiliation(s)
- Dalia Shallom
- Department of Food Engineering and Biotechnology and Institute of Catalysis, Science and Technology, Technion, Haifa 32000, Israel
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292
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Ulgar V, López Ó, Maya I, Fernández-Bolaños JG, Bols M. Synthesis of furan 4′-thio-C-nucleosides, their methylsulfonium and sulfoxide derivatives. Evaluation as glycosidase inhibitors. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00339-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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293
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Nerinckx W, Desmet T, Claeyssens M. A hydrophobic platform as a mechanistically relevant transition state stabilising factor appears to be present in the active centre of all glycoside hydrolases. FEBS Lett 2003; 538:1-7. [PMID: 12633843 DOI: 10.1016/s0014-5793(03)00148-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An in silico survey of the -1 subsite of all known 3D-structures of O-glycoside hydrolases containing a suitably positioned ligand has led to the recognition -- apparently without exceptions -- of a transition state stabilising hydrophobic platform which is complementary to a crucial hydrophobic patch of the ligand. This platform is family-specific and highly conserved. A comprehensive list is given with examples of enzymes belonging to 33 different families. Several typical constellations of platform - protein residues are described.
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Affiliation(s)
- W Nerinckx
- Department of Biochemistry, Physiology and Microbiology, Ghent University, K L Ledeganckstraat 35, B-9000 Gent, Belgium.
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294
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Laitinen T, Rouvinen J, Peräkylä M. MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)–substrate complexes: binding of the reactive sugar in a skew boat and chair conformation. Org Biomol Chem 2003; 1:3535-40. [PMID: 14599014 DOI: 10.1039/b307335a] [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: 11/21/2022]
Abstract
The binding of xylotetraose in different conformations to the active site of endo-1,4-beta-xylanase II (XynII) from Trichoderma reesei was studied using molecular dynamics (MD) simulations and free energy analyses employing the MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Surface Area) method. MD simulations of 1 ns were done for the substrate xylotetraose having the reactive sugar, which is bound in the -1 subsite of XynII in the 4C1 (chair) and 2So (skew boat) ground state conformations, and for the transition state of the XynII catalysed hydrolysis of the beta-glycosidic linkage. According to the simulations and free energy analysis, XynII binds the substrate with the -1 sugar in the 2So conformation 59.8 kJ mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. The reactive 2So conformation resembles closely the reaction transition state and has the breaking glycosidic bond in a pseudo-axial orientation ready for facile bond cleavage. The transition state was calculated to be bound 77.1 kJ mol(-1) tighter than the 4C1 ground state conformation. The molecular mechanical interaction energy between the enzyme and the reactive pyranoside unit at the -1 subsite was 75.7 kJ mol(-1) more favorable for the binding of the 2So conformation than the 2C1 conformation, explaining the clearly tighter binding of the reactive structure The results of this study indicate that in the Michaelis complex XynII, a member of the family 11 xylanase, the substrate is bound in a skew boat conformation and in the catalytic reaction, the -1 sugar proceeds from the 4C1 conformation through 2So to the transition state with the -1 sugar in the 2,5B conformation.
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Affiliation(s)
- Tuomo Laitinen
- Department of Chemistry, University of Kuopio, PO Box 1627, FIN-70211 Kuopio, Finland
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Advances in Chemical Synthesis of Carbasugars and Analogues. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1572-5995(03)80013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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