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Twisting of Glycosidic Bonds by Hydrolases

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Twisting of Glycosidic Bonds by Hydrolases Carbohydrate Research 344 (2009) 2157–2166 Contents lists available at ScienceDirect Carbohydrate Research journal homepage: www.elsevier.com/locate/carres Twisting of glycosidic bonds by hydrolases Glenn P. Johnson a, , Luis Petersen b, , Alfred D. French a, Peter J. Reilly b,* a Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124-4305, USA b Department of Chemical and Biological Engineering, 2114 Sweeney Hall, Iowa State University, Ames, IA 50011-2230, USA article info abstract Article history: Patterns of scissile bond twisting have been found in crystal structures of glycoside hydrolases (GHs) that Received 6 July 2009 are complexed with substrates and inhibitors. To estimate the increased potential energy in the sub- Received in revised form 7 August 2009 strates that results from this twisting, we have plotted torsion angles for the scissile bonds on hybrid Accepted 11 August 2009 Quantum Mechanics::Molecular Mechanics energy surfaces. Eight such maps were constructed, including Available online 14 August 2009 one for a-maltose and three for different forms of methyl a-acarviosinide to provide energies for twisting of a-(1,4) glycosidic bonds. Maps were also made for b-thiocellobiose and for three b-cellobiose conform- Keywords: ers having different glycon ring shapes to model distortions of b-(1,4) glycosidic bonds. Different GH fam- Conformational analysis ilies twist scissile glycosidic bonds differently, increasing their potential energies from 0.5 to 9.5 kcal/ Glycoside hydrolases Glycosidic bonds mol. In general, the direction of twisting of the glycosidic bond away from the conformation of lowest Intramolecular energy intramolecular energy correlates with the position (syn or anti) of the proton donor with respect to the Molecular mechanics glycon’s ring oxygen atom. This correlation suggests that glycosidic bond distortion is important for Quantum mechanics the optimal orientation of one of the glycosidic oxygen lone pairs toward the enzyme’s proton donor. Ó 2009 Elsevier Ltd. All rights reserved. 1. Introduction energy barrier to cleavage, although strain was ruled out as the ma- jor contribution toward lowering the reaction barrier. Electrostatic It has been known for many years that the substrate carbohy- interactions are proposed to have a more important role.7 drate residue located immediately to the non-reducing side of There is now a sufficient number of GH crystal structures with the scissile glycosidic bond (in enzyme subsite À1) is distorted carbohydrates bound in active sites to address the question of the during the cleavage reaction catalyzed by many glycoside effect of GH–ligand binding on scissile bond geometry. Our ap- hydrolases (GHs).1 Evidence of ring conformations of higher intra- proach was to plot the available data for different a- and b-glyco- 4 molecular energy than for the optimal C1 shape has become sidic linkages involving nitrogen, oxygen, and sulfur [NOS] on overwhelming in recent years as crystal structures of GH–ligand maps of EIntra values. Thus, we have plotted experimental values complexes have been solved.2,3 of / (O50–C10–[NOS]4–C4) and w (C10–[NOS]4–C4–C5) (Fig. 1)on A second distortion, that of the torsion angles for the two bonds energy surfaces that are based on hybrid Quantum Mechan- connected to the glycosidic oxygen atom, has been discussed much ics::Molecular Mechanics (QM::MM) computations in an attempt less. One article was devoted to twisting distortions for all linkages to gain new insights on this question. in oligo- and polysaccharides bound by proteins.4 Most linkages had low-energy conformations, but some scissile linkages corre- sponded to high energies. Distortion of substrate torsion angles 2. Glycoside hydrolase families and mechanisms by GHs was also mentioned by Fujimoto et al.5 Several different cleavage functions could be enhanced by twist- GHs have been classified into >100 families based on similar- 8 ing glycosidic bonds. Distortion of the scissile bond can improve ac- ities in their primary structures. Tertiary structures, that is, the cess of the catalytic amino acid residues to the glycosidic oxygen overall arrangement of helices, strands, and loops, are expected atom and the C10 atom of the non-reducing-side carbohydrate resi- to be quite similar within individual families. Crystal structures due. Changes in the electronic structure resulting from torsional are known for enzymes with a ligand bound in subsites À1 and 6 changes could enhance reactivity. Also, an increase of EIntra, the rel- +1 that belong to 14 families that cleave either a-1,4 or b-1,4 gly- ative intramolecular energy above that for the lowest-energy con- cosidic bonds. These subsites contain the glycosyl residues to the formation of the scissile bond torsion angles, could reduce the immediate non-reducing and reducing sides, the glycon and aglycon, respectively, of the scissile glycosidic bond (Table 1 and Supplementary data). Members of five families hydrolyze * Corresponding author. Tel.: +1 515 294 5968; fax: +1 515 294 2689. E-mail address: [email protected] (P.J. Reilly). a-glycosidic bonds, while members of the other nine cleave Contributed equally to the work. b-glycosidic bonds. 0008-6215/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.carres.2009.08.011 2158 G. P. Johnson et al. / Carbohydrate Research 344 (2009) 2157–2166 Maltose Cellobiose 4C O5’ 4C 4C 1 1 1 C1’ O4 C4 4C 1 C5 4C 1 2S O Methyl -acarviosinide 2H 3 4C 1 4C Thiocellobiose 1 4C 1 1S 4C 3 1 Figure 1. Structures of molecules used to construct energy contour maps. Ring conformations are denoted with labels. Superscripts and subscripts denote the atoms above or below the plane of the ring, respectively. Occasionally, different GH families appear to be distantly re- ken and a hydroxyl group from the coordinated water molecule re- lated to each other by having similar tertiary structures and mech- places it, inverting the configuration of the carbohydrate residue. anisms, and therefore they are grouped into clans.8 Among the The remaining proton from the water molecule is accepted by families listed in Table 1, GH families 2 and 5 (GH2 and GH5) are the dissociated carboxyl group. part of Clan GH-A, while GH13 and GH77 belong to Clan GH-H. In the retaining mechanism, the protonated carboxyl group do- Other families listed in Table 1 are either the only representatives nates a proton to the glycosidic oxygen atom, and the dissociated of their clans with known tertiary structures containing glucosyl or carboxyl group forms a covalent bond with the C10 atom. The bond acarbose-derived carbohydrate ligands in subsites À1 and +1, or between the C10 atom and the glycosidic oxygen atom is broken they have not been classified into clans. and a hydroxyl group from the water molecule hydrates the C10 GHs hydrolyze glycosidic bonds by two general mechanisms,9 atom, breaking the covalent bond with the carboxyl group. This with some exceptions. In the inverting mechanism, a carboxyl double-displacement reaction retains the anomeric configuration group on an amino acid side-chain donates a proton to the scissile of the glycon. Of the families listed in Table 1, five have inverting glycosidic oxygen atom. Meanwhile, the oxygen atom of a water mechanisms and nine have retaining mechanisms. molecule coordinated by a dissociated carboxyl group on a second The protonated carboxyl group is usually positioned laterally on amino acid side-chain forms a partial bond with the C10 atom of the either side of the O4 atom (the glycosidic oxygen atom). The differ- carbohydrate ring in subsite À1. The complex proceeds through ent positions of the proton donor are labeled as syn or anti.10 the transition state with the bond between O50 and C10 atoms Syn-proton donors are on the same side as the O50 atom (the glycon assuming partial double bond character. This causes the C50–O50– ring oxygen atom), while anti proton donors are on the opposite C10–C20 atoms to form a plane. Finally, the glycosidic bond is bro- side (Fig. 2). Table 1 GH families containing enzymes with crystal structures of oligosaccharides bound in subsites À1 and +1 GH GH GH family members No. of Catalytic Ligand glycon Ligand bond Position of family clan structures mechanism conformation configuration proton donor 4 2Ab-Galactosidase 1 R C1 b-(1,4) anti 4 3—b-Glucan glucohydrolase 2 R C1 b-(1,4) anti 4 5 A Endocellulase, EG 4 R C1 b-(1,4) anti 4 2 6 — CBH, EG 3 I C1, SO b-(1,4) syn 7 B CBH, EG 1 R Distorted 1,4B b-(1,4) syn 8MEG 1I 2,5B b-(1,4) anti 9 — CBH 1 I 4E b-(1,4) syn 1 12 C EG 2R S3 b-(1,4) syn 2 4 13 H CGTase, a-amylase, neopullulanase, glucan 1,4-a-maltohexaosidase, 42 R H3, C1 a-(1,4) syn amylosucrase, 4-a-glucanotransferase, maltogenic amylase 4 14 — b-Amylase 4 I C1 a-(1,4) syn 2 2 15 L Glucoamylase, glucodextranase 5 I H3, E a-(1,4) syn 1 44 — EG 1R S3 b-(1,4) anti 2 57 — 4-a-Glucanotransferase 1 R H3 a-(1,4) anti 4 77 H 4-a-Glucanotransferase 1 R C1 a-(1,4) anti Abbreviations: CBH: cellobiohydrolase; CGTase: cyclomaltodextrin glucanotransferase; EG: endo-1,4-b-glucanase; GH: glycoside hydrolase; I: inverting; R: retaining. G. P. Johnson et al. / Carbohydrate Research 344 (2009) 2157–2166 2159 Figure 2. The different locations of the proton donor in glycoside hydrolases. The proton donor is labeled as syn if it is on the same side of the glycon ring oxygen atom.
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