Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation

Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

doi:10.1074/jbc.m111.297713

Cited by 109 publications

(127 citation statements)

References 82 publications

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“…The consensus mechanism for glycoside hydrolases involves one amino acid residue to serve as a proton donor and another to act as a nucleophile (47). The preponderance of aromatic residues in glycoside hydrolases has been attributed to a central role in substrate recognition and binding (48)(49)(50). No redox function has been identified in most of these enzymes, and it is probable that long Tyr/Trp chains are involved simply in substrate recognition and binding as well as fold stability.…”

Section: Resultsmentioning

confidence: 99%

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

Gray

2015

Proc. Natl. Acad. Sci. U.S.A.

219

285

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Living organisms have adapted to atmospheric dioxygen by exploiting its oxidizing power while protecting themselves against toxic side effects. Reactive oxygen and nitrogen species formed during oxidative stress, as well as high-potential reactive intermediates formed during enzymatic catalysis, could rapidly and irreversibly damage polypeptides were protective mechanisms not available. Chains of redox-active tyrosine and tryptophan residues can transport potentially damaging oxidizing equivalents (holes) away from fragile active sites and toward protein surfaces where they can be scavenged by cellular reductants. Precise positioning of these chains is required to provide effective protection without inhibiting normal function. A search of the structural database reveals that about one third of all proteins contain Tyr/Trp chains composed of three or more residues. Although these chains are distributed among all enzyme classes, they appear with greatest frequency in the oxidoreductases and hydrolases. Consistent with a redox-protective role, approximately half of the dioxygen-using oxidoreductases have Tyr/Trp chain lengths ≥3 residues. Among the hydrolases, long Tyr/Trp chains appear almost exclusively in the glycoside hydrolases. These chains likely are important for substrate binding and positioning, but a secondary redox role also is a possibility.iron oxygenases | electron transfer | reactive oxygen species | superoxide dismutase | cytochrome P450

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Section: Resultsmentioning

confidence: 99%

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

Gray

2015

Proc. Natl. Acad. Sci. U.S.A.

219

285

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“…2A). In addition to the steric constraints of the tunnel, carbohydrate-interactions of aromatic residues lining the substrate-binding clefts are important for processivity and, more generally, may make large contributions to the ligand binding free energy (21,22,25,26,28,(62)(63)(64)(65). Notably, ChiC2 has fewer such aromatic residues than ChiA and ChiB, primarily affecting the product subsites (Fig.…”

Section: Discussionmentioning

confidence: 99%

Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases

Payne

Baban

Horn

et al. 2012

Journal of Biological Chemistry

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112

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Background: Nature employs processive and nonprocessive glycoside hydrolases to degrade polysaccharides. Results: We solved the Serratia marcescens nonprocessive chitinase (ChiC2) structure and used simulation to identify dynamic hallmarks of processivity in S. marcescens chitinases. Conclusion: Dynamic metrics complement structural insights in determining processivity. Significance: Identification of hallmarks of processivity is a key step toward development of a general, molecular-level theory of glycoside hydrolase processivity.

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“…1F, the glucopyranose residue at the −7 site forms a transition region between the cellulose chain in the enzyme and the crystal. GHs that bind carbohydrate polymers typically use aromatic-carbohydrate interactions along active site tunnels or clefts (31)(32)(33)(34)(35). GH7s contain a conserved tryptophan residue, Trp40 in TrCel7A, which binds to the glucopyranose ring at the −7 site in GH7 structures (31).…”

Section: Simulations Predictmentioning

confidence: 99%

Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose

Payne

Resch

Chen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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160

147

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Plant cell-wall polysaccharides represent a vast source of food in nature. To depolymerize polysaccharides to soluble sugars, many organisms use multifunctional enzyme mixtures consisting of glycoside hydrolases, lytic polysaccharide mono-oxygenases, polysaccharide lyases, and carbohydrate esterases, as well as accessory, redox-active enzymes for lignin depolymerization. Many of these enzymes that degrade lignocellulose are multimodular with carbohydrate-binding modules (CBMs) and catalytic domains connected by flexible, glycosylated linkers. These linkers have long been thought to simply serve as a tether between structured domains or to act in an inchworm-like fashion during catalytic action. To examine linker function, we performed molecular dynamics (MD) simulations of the Trichoderma reesei Family 6 and Family 7 cellobiohydrolases (TrCel6A and TrCel7A, respectively) bound to cellulose. During these simulations, the glycosylated linkers bind directly to cellulose, suggesting a previously unknown role in enzyme action. The prediction from the MD simulations was examined experimentally by measuring the binding affinity of the Cel7A CBM and the natively glycosylated Cel7A CBM-linker. On crystalline cellulose, the glycosylated linker enhances the binding affinity over the CBM alone by an order of magnitude. The MD simulations before and after binding of the linker also suggest that the bound linker may affect enzyme action due to significant damping in the enzyme fluctuations. Together, these results suggest that glycosylated linkers in carbohydrate-active enzymes, which are intrinsically disordered proteins in solution, aid in dynamic binding during the enzymatic deconstruction of plant cell walls. biofuels | cellulase | post-translational modification | carbohydrate recognition

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Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation

Cited by 109 publications

References 82 publications

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases

Glycosylated linkers in multimodular lignocellulose-degrading enzymes dynamically bind to cellulose

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