Computational study on the carboligation reaction of acetohidroxyacid synthase: New approach on the role of the HEThDP - intermediate

Gonzalo Jaña, Verónica Jiménez, Jordi Villà-Freixa, Xavier Prat-Resina, Eduardo Delgado, Joel Alderete

Resultado de la investigación: Article

12 Citas (Scopus)

Resumen

Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP -). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP - from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP - has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP") and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acidbase properties of the HEThDP" intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP" intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle.

Idioma originalEnglish
Páginas (desde-hasta)1774-1788
Número de páginas15
PublicaciónProteins: Structure, Function and Bioinformatics
Volumen78
N.º7
DOI
EstadoPublished - 28 abr 2010

Huella dactilar

Pyruvic Acid
Thiamine Pyrophosphate
Molecular Dynamics Simulation
Molecular dynamics
Catalytic Domain
Reaction intermediates
Decarboxylation
Enzymes
Yeast
Anions
Yeasts
Molecules
Acids
Computer simulation
alpha-acetolactate

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Citar esto

@article{f428be952e9b4823bff233fbdac1847e,
title = "Computational study on the carboligation reaction of acetohidroxyacid synthase: New approach on the role of the HEThDP - intermediate",
abstract = "Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP -). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP - from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP - has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP{"}) and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acidbase properties of the HEThDP{"} intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP{"} intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle.",
keywords = "AHAS, Molecular dynamics, Semiempirical calculations, Thiamin diphosphate",
author = "Gonzalo Ja{\~n}a and Ver{\'o}nica Jim{\'e}nez and Jordi Vill{\`a}-Freixa and Xavier Prat-Resina and Eduardo Delgado and Joel Alderete",
year = "2010",
month = "4",
day = "28",
doi = "10.1002/prot.22693",
language = "English",
volume = "78",
pages = "1774--1788",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "7",

}

Computational study on the carboligation reaction of acetohidroxyacid synthase : New approach on the role of the HEThDP - intermediate. / Jaña, Gonzalo; Jiménez, Verónica; Villà-Freixa, Jordi; Prat-Resina, Xavier; Delgado, Eduardo; Alderete, Joel.

En: Proteins: Structure, Function and Bioinformatics, Vol. 78, N.º 7, 28.04.2010, p. 1774-1788.

Resultado de la investigación: Article

TY - JOUR

T1 - Computational study on the carboligation reaction of acetohidroxyacid synthase

T2 - New approach on the role of the HEThDP - intermediate

AU - Jaña, Gonzalo

AU - Jiménez, Verónica

AU - Villà-Freixa, Jordi

AU - Prat-Resina, Xavier

AU - Delgado, Eduardo

AU - Alderete, Joel

PY - 2010/4/28

Y1 - 2010/4/28

N2 - Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP -). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP - from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP - has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP") and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acidbase properties of the HEThDP" intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP" intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle.

AB - Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP -). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP - from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP - has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP") and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acidbase properties of the HEThDP" intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP" intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle.

KW - AHAS

KW - Molecular dynamics

KW - Semiempirical calculations

KW - Thiamin diphosphate

UR - http://www.scopus.com/inward/record.url?scp=77951236498&partnerID=8YFLogxK

U2 - 10.1002/prot.22693

DO - 10.1002/prot.22693

M3 - Article

C2 - 20225259

AN - SCOPUS:77951236498

VL - 78

SP - 1774

EP - 1788

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

SN - 0887-3585

IS - 7

ER -