Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

Takashi Kamachi, Tetsuo Toraya, Kazunari Yoshizawa

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

A mutation analysis of the catalytic functions of active-site residues of coenzyme B12-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol-1 in the wild-type enzyme. The highest activation energy, 19.6 kcal mol-1, was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mo-1 for OH migration in the Glu 170Ala mutant is only 2.1 kcal mol-1 higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO- groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.

Original languageEnglish
Pages (from-to)7864-7873
Number of pages10
JournalChemistry - A European Journal
Volume13
Issue number28
DOIs
Publication statusPublished - Oct 16 2007

Fingerprint

Propanediol Dehydratase
Coenzymes
Propylene Glycols
Catalysis
Hydrogen
Propylene Glycol
Activation energy
Chemical activation
Hydrogen bonds
Enzymes
Deprotonation
Protons
cobamamide

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Organic Chemistry

Cite this

Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase. / Kamachi, Takashi; Toraya, Tetsuo; Yoshizawa, Kazunari.

In: Chemistry - A European Journal, Vol. 13, No. 28, 16.10.2007, p. 7864-7873.

Research output: Contribution to journalArticle

@article{452761127d9a4a2fa2aead88bd396ea4,
title = "Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase",
abstract = "A mutation analysis of the catalytic functions of active-site residues of coenzyme B12-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol-1 in the wild-type enzyme. The highest activation energy, 19.6 kcal mol-1, was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mo-1 for OH migration in the Glu 170Ala mutant is only 2.1 kcal mol-1 higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO- groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.",
author = "Takashi Kamachi and Tetsuo Toraya and Kazunari Yoshizawa",
year = "2007",
month = "10",
day = "16",
doi = "10.1002/chem.200601466",
language = "English",
volume = "13",
pages = "7864--7873",
journal = "Chemistry - A European Journal",
issn = "0947-6539",
publisher = "Wiley-VCH Verlag",
number = "28",

}

TY - JOUR

T1 - Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

AU - Kamachi, Takashi

AU - Toraya, Tetsuo

AU - Yoshizawa, Kazunari

PY - 2007/10/16

Y1 - 2007/10/16

N2 - A mutation analysis of the catalytic functions of active-site residues of coenzyme B12-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol-1 in the wild-type enzyme. The highest activation energy, 19.6 kcal mol-1, was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mo-1 for OH migration in the Glu 170Ala mutant is only 2.1 kcal mol-1 higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO- groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.

AB - A mutation analysis of the catalytic functions of active-site residues of coenzyme B12-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol-1 in the wild-type enzyme. The highest activation energy, 19.6 kcal mol-1, was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mo-1 for OH migration in the Glu 170Ala mutant is only 2.1 kcal mol-1 higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO- groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.

UR - http://www.scopus.com/inward/record.url?scp=35048840694&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=35048840694&partnerID=8YFLogxK

U2 - 10.1002/chem.200601466

DO - 10.1002/chem.200601466

M3 - Article

C2 - 17614304

AN - SCOPUS:35048840694

VL - 13

SP - 7864

EP - 7873

JO - Chemistry - A European Journal

JF - Chemistry - A European Journal

SN - 0947-6539

IS - 28

ER -