Dataset Information

Mutations close to a hub residue affect the distant active site of a GH1 ?-glucosidase.

ABSTRACT: The tertiary structure of proteins has been represented as a network, in which residues are nodes and their contacts are edges. Protein structure networks contain residues, called hubs or central, which are essential to form short connection pathways between any pair of nodes. Hence hub residues may effectively spread structural perturbations through the protein. To test whether modifications nearby to hub residues could affect the enzyme active site, mutations were introduced in the ?-glycosidase Sf?gly (PDB-ID: 5CG0) directed to residues that form an ?-helix (260-265) and a ?-strand (335-337) close to one of its main hub residues, F251, which is approximately 14 Å from the Sf?gly active site. Replacement of residues A263 and A264, which side-chains project from the ?-helix towards F251, decreased the rate of substrate hydrolysis. Mutation A263F was shown to weaken noncovalent interactions involved in transition state stabilization within the Sf?gly active site. Mutations placed on the opposite side of the same ?-helix did not show these effects. Consistently, replacement of V336, which side-chain protrudes from a ?-strand face towards F251, inactivated Sf?gly. Next to V336, mutation S337F also caused a decrease in noncovalent interactions involved in transition state stabilization. Therefore, we suggest that mutations A263F, A264F, V336F and S337F may directly perturb the position of the hub F251, which could propagate these perturbations into the Sf?gly active site through short connection pathways along the protein network.

SUBMITTER: Souza VP

PROVIDER: S-EPMC5991390 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Mutations close to a hub residue affect the distant active site of a GH1 β-glucosidase.

Souza Valquiria P VP Ikegami Cecília M CM Arantes Guilherme M GM Marana Sandro R SR

PloS one 20180606 6

The tertiary structure of proteins has been represented as a network, in which residues are nodes and their contacts are edges. Protein structure networks contain residues, called hubs or central, which are essential to form short connection pathways between any pair of nodes. Hence hub residues may effectively spread structural perturbations through the protein. To test whether modifications nearby to hub residues could affect the enzyme active site, mutations were introduced in the β-glycosida ...[more]

PMID: 29874288

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Project description:European honeybee, Apis mellifera, produces ?-glucosidase (HBGase) that catalyzes the cleavage of an ?-glycosidic bond of the non-reducing end of polysaccharides and has potential applications for malt hydrolysis in brewing industry. Characterized by their substrate specificities, HBGases have three isoforms including HBGase II, which prefers maltose to sucrose as a substrate. Previous study found that the catalytic efficiency of maltose hydrolysis of N226P mutant of HBGase II was higher than that of the wild type (WT), and the catalytic efficiency of maltose hydrolysis of WT was higher than those of H227Y and N226P-H227Y mutants. We hypothesized that N226P mutation probably caused maltose to bind with better affinity and position/orientation for hydrolysis than WT, while H227Y and N226P-H227Y mutations caused maltose to bind with worse affinity and position/orientation for hydrolysis than WT. Using this hypothesis, we performed molecular dynamics on the catalytically competent binding conformations of maltose/WT, maltose/N226P, maltose/H227Y, and maltose/N226P-H227Y complexes to elucidate effects of N226P and H227Y mutations on maltose binding in HBGase II active site. Our results reasonably support this hypothesis because the N226P mutant had better binding affinity, higher number of important binding residues, strong and medium hydrogen bonds as well as shorter distance between atoms necessary for hydrolysis than WT, while the H227Y and N226P-H227Y mutants had worse binding affinities, lower number of important binding residues and strong hydrogen bonds as well as longer distances between atoms necessary for hydrolysis than WT. Moreover, results of binding free energy and hydrogen bond interaction of residue 227 support the role of H227 as a maltose preference residue, as proposed by previous studies. Our study provides important and novel insight into how N226P and H227Y mutations affect maltose binding in HBGase II active site. This knowledge could potentially be used to engineer HBGase II to improve its efficiency.

Dataset Information

Mutations close to a hub residue affect the distant active site of a GH1 ?-glucosidase.

Publications

Mutations close to a hub residue affect the distant active site of a GH1 β-glucosidase.

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