Catalytic Reaction Mechanism Based on α-Secondary Deuterium Isotope Effects in Hydrolysis of Trehalose by European Honeybee Trehalase

Mori, Haruhide; Lee, Jin Ha; Okuyama, Masayuki; Nishimoto, Mamoru; Ohguchi, Masao; Kim, Doman; Kimura, Atsuo; Chiba, Seiya

doi:10.1271/bbb.90447

Cited by 21 publications

(17 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The transition states depicted in Fig. 3A and B are similar to those of the S N 2-like reaction, 14) but such transition states are impossible due to improbability of direct attack on the C 1 -carbon by water at the initial stage of the hydrolysis of acetal molecule. Consequently, it is inferred that there are actually no reaction depend on both nucleophilic single and double displacement mechanisms.…”

Section: Nucleophilic Displacement Reaction Mechanismsmentioning

confidence: 81%

See 1 more Smart Citation

A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

Chiba

2012

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

Various catalytic reaction models have been proposed as the reaction mechanisms of glycosidases, but a reasonable and unitary model capable of interpreting both ''inverting'' and ''retaining'' glycosidase reactions remains to be established. As for the models proposed to date, the nucleophilic displacement mechanism and the oxocarbenium ion intermediate mechanism are widely known, but recently the former is widely accepted, and so the general tendency of world opinion appears to favor it. This reaction model, however, is considered to comprise some inconsistencies that cannot be neglected from the viewpoint of reactivity in organic chemistry. While the nucleophilic displacement mechanism is often applied to reactions of glycosidases, it appears unlikely that such reactions actually occur. This review argues that the oxocarbenium ion intermediate reaction mechanism is more rational than the nucleophilic displacement reaction mechanism, as the action mode of glycosidases and related enzymes.

show abstract

Section: Nucleophilic Displacement Reaction Mechanismsmentioning

confidence: 81%

“…2,3,14) The natural carbohydrate as the substrate of glycosidase is acetal molecule. The process of hydrolytic reaction of acetal molecule is shown in Fig.…”

Section: Hydrolytic Reaction From Acetal To Hemiacetalmentioning

confidence: 99%

A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

Chiba

2012

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…This canonical double-displacement mechanism has been challenged by proponents of the oxocarbenium ion intermediate mechanism, in which the general acid-assisted departure of an aglycon leaving group leads to a short-lived, planar carbocation on C1 of the glycon, which is then hydrated by an incoming H 2 O with an estimated rate constant of 10 12 s −1 (16). Each mechanism draws support from different types of experimental and computational evidence (17)(18)(19)(20)(21)(22), with the double-displacement mechanism being generally accepted.…”

mentioning

confidence: 99%

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

Wan

Parks

Hanson

et al. 2015

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

View full text Add to dashboard Cite

Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pK a values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pK a values of the catalytic Glu residues in both the apo-and substrate-bound states of the enzyme. The calculated pK a of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.glycoside hydrolase | protonation state | macromolecular neutron crystallography | xylanase | molecular simulations

show abstract

“…E. coli Tre37A is composed of a small α-helical domain at the N-terminal and a catalytic (α/α) 6 barrel domain at the C-terminal. Studies performed using deuterium-labeled trehalose have shown that the catalytic reaction of a GH37 trehalase from the European honeybee occurs by the oxocarbenium ion intermediate mechanism (28).…”

Section: Enzymes Classified Into Clan Gh-g: Trehalase Processing mentioning

confidence: 99%

Structural Similarity between a Starch-hydrolyzing Enzyme and an N-Glycan-Hydrolyzing Enzyme: Exohydrolases Cleaving α-1,X-Glucosidic Linkages to Produce β-Glucose

Tonozuka

Miyazaki

Nishikawa

2011

TIGG

View full text Add to dashboard Cite

Glucoamylase, glucodextranase, trehalase, and eukaryotic N-glycan processing α-glucosidase I have been identified as exo-acting enzymes that hydrolyze α-1,Xglucosidic linkages from the non-reducing end to produce β-glucose. While the physiological functions of these enzymes are different, they share a catalytic (α/α) 6 barrel domain and show many structural similarities. These enzymes, with few exceptions, belong to the glycoside hydrolase families (GHs) 15, 37, and 63 in the CAZy database, and all these enzymes have 2 conserved aspartic or glutamic acid residues in the catalytic domain. The observations led us to consider that the group of GH15, GH37, and GH63 may be designated as a "glucoamylase family." There are also many hydrolases and phosphorylases structurally related to GH15, GH37, and GH63.

show abstract

Catalytic Reaction Mechanism Based on α-Secondary Deuterium Isotope Effects in Hydrolysis of Trehalose by European Honeybee Trehalase

Cited by 21 publications

References 52 publications

A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

Structural Similarity between a Starch-hydrolyzing Enzyme and an N-Glycan-Hydrolyzing Enzyme: Exohydrolases Cleaving α-1,X-Glucosidic Linkages to Produce β-Glucose

Contact Info

Product

Resources

About