Catalytic roles of active-site amino acid residues of coenzyme B 12-dependent diol dehydratase

Protonation state of histidine and pull effect of glutamate

Takashi Kamachi, Tetsuo Toraya, Kazunari Yoshizawa

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu 170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model, QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.

Original languageEnglish
Pages (from-to)16207-16216
Number of pages10
JournalJournal of the American Chemical Society
Volume126
Issue number49
DOIs
Publication statusPublished - Dec 15 2004

Fingerprint

Propanediol Dehydratase
Coenzymes
Protonation
Histidine
Amino acids
Glutamic Acid
Hydrogen
Catalytic Domain
Amino Acids
Hydrogen Bonding
Protons
Ions
Water
Enzymes
Substrates
7-mercaptoheptanoylthreonine phosphate
Hydrogen bonds
Activation energy
Chemical activation

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

@article{0b4d785e30174b358a221ab10b0f2b56,
title = "Catalytic roles of active-site amino acid residues of coenzyme B 12-dependent diol dehydratase: Protonation state of histidine and pull effect of glutamate",
abstract = "The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu 170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model, QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.",
author = "Takashi Kamachi and Tetsuo Toraya and Kazunari Yoshizawa",
year = "2004",
month = "12",
day = "15",
doi = "10.1021/ja045572o",
language = "English",
volume = "126",
pages = "16207--16216",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "49",

}

TY - JOUR

T1 - Catalytic roles of active-site amino acid residues of coenzyme B 12-dependent diol dehydratase

T2 - Protonation state of histidine and pull effect of glutamate

AU - Kamachi, Takashi

AU - Toraya, Tetsuo

AU - Yoshizawa, Kazunari

PY - 2004/12/15

Y1 - 2004/12/15

N2 - The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu 170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model, QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.

AB - The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu 170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model, QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.

UR - http://www.scopus.com/inward/record.url?scp=10344257551&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=10344257551&partnerID=8YFLogxK

U2 - 10.1021/ja045572o

DO - 10.1021/ja045572o

M3 - Article

VL - 126

SP - 16207

EP - 16216

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 49

ER -