Active site model for γ-aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities

M. D. Toney, S. Pascarella, D. De Biase

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

A homology model for the pig isozyme of the pyridoxal phosphate-dependent enzyme γ-aminobutyrate (GABA) aminotransferase has been built based mainly on the structure of dialkylglycine decarboxylase and on a multiple sequence alignment of 28 evolutionarily related enzymes. The proposed active site structure is presented and analyzed. Hypothetical structures for external aldimine intermediates explain several characteristics of the enzyme. In the GABA external aldimine model, the pro-S proton at C4 of GABA, which abstracted in the 1,3-azaallylic rearrangement interconverting the aldimine and ketimine intermediates, is oriented perpendicular to the plane of the pyridoxal phosphate ring. Lys 329 is in close proximity and is probably the general base catalyst for the proton transfer reaction. The carboxylate group of GABA interacts with Arg 192 and Lys 203, which determine the specificity of the enzyme for monocarboxylic ω-amino acids such as GABA. In the proposed structure for the L-glutamate external aldimine, the α-carboxylate interacts with Arg 445. Glu 265 is proposed to interact with this same arginine in the GABA external aldimine, enabling the enzyme to act on ω-amino acids in one half-reaction and on α-amino acids in the other. The reactivities of inhibitors are well explained by the proposed active site structure. The R and S isomers of β-substituted phenyl and p-chlorophenyl GABA would bind in very different modes due to differential steric interactions, with the reactive S isomer leaving the orientation of the GABA moiety relatively unperturbed compared to that of the natural substrate. In our model, only the reactive S isomer of the mechanism based inhibitor vinyl-GABA, an effective anti-epileptic drug known clinically as Vigabatrin, would orient the scissile C4-H bond perpendicular to the coenzyme ring plane and present the proton to Lys 329, the proposed general base catalyst of the reaction. The R isomer would direct the vinyl group toward Lys 329 and the C4-H bond toward Arg 445. The active site model presented provides a basis for site-directed mutagenesis and drug design experiments.

Original languageEnglish (US)
Pages (from-to)2366-2374
Number of pages9
JournalProtein Science
Volume4
Issue number11
StatePublished - 1995
Externally publishedYes

Fingerprint

4-Aminobutyrate Transaminase
Substrate Specificity
gamma-Aminobutyric Acid
Catalytic Domain
Isomers
Substrates
Enzymes
Protons
2,2-dialkylglycine decarboxylase
Pyridoxal Phosphate
Amino Acids
Vigabatrin
Aminobutyrates
Mutagenesis
Baclofen
Catalysts
Proton transfer
Sequence Alignment
Drug Design
Coenzymes

Keywords

  • γ-aminobutyrate aminotransferase
  • GABA
  • homology modeling
  • pyridoxal phosphate
  • Vigabatrin

ASJC Scopus subject areas

  • Biochemistry

Cite this

Active site model for γ-aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities. / Toney, M. D.; Pascarella, S.; De Biase, D.

In: Protein Science, Vol. 4, No. 11, 1995, p. 2366-2374.

Research output: Contribution to journalArticle

Toney, M. D. ; Pascarella, S. ; De Biase, D. / Active site model for γ-aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities. In: Protein Science. 1995 ; Vol. 4, No. 11. pp. 2366-2374.
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N2 - A homology model for the pig isozyme of the pyridoxal phosphate-dependent enzyme γ-aminobutyrate (GABA) aminotransferase has been built based mainly on the structure of dialkylglycine decarboxylase and on a multiple sequence alignment of 28 evolutionarily related enzymes. The proposed active site structure is presented and analyzed. Hypothetical structures for external aldimine intermediates explain several characteristics of the enzyme. In the GABA external aldimine model, the pro-S proton at C4 of GABA, which abstracted in the 1,3-azaallylic rearrangement interconverting the aldimine and ketimine intermediates, is oriented perpendicular to the plane of the pyridoxal phosphate ring. Lys 329 is in close proximity and is probably the general base catalyst for the proton transfer reaction. The carboxylate group of GABA interacts with Arg 192 and Lys 203, which determine the specificity of the enzyme for monocarboxylic ω-amino acids such as GABA. In the proposed structure for the L-glutamate external aldimine, the α-carboxylate interacts with Arg 445. Glu 265 is proposed to interact with this same arginine in the GABA external aldimine, enabling the enzyme to act on ω-amino acids in one half-reaction and on α-amino acids in the other. The reactivities of inhibitors are well explained by the proposed active site structure. The R and S isomers of β-substituted phenyl and p-chlorophenyl GABA would bind in very different modes due to differential steric interactions, with the reactive S isomer leaving the orientation of the GABA moiety relatively unperturbed compared to that of the natural substrate. In our model, only the reactive S isomer of the mechanism based inhibitor vinyl-GABA, an effective anti-epileptic drug known clinically as Vigabatrin, would orient the scissile C4-H bond perpendicular to the coenzyme ring plane and present the proton to Lys 329, the proposed general base catalyst of the reaction. The R isomer would direct the vinyl group toward Lys 329 and the C4-H bond toward Arg 445. The active site model presented provides a basis for site-directed mutagenesis and drug design experiments.

AB - A homology model for the pig isozyme of the pyridoxal phosphate-dependent enzyme γ-aminobutyrate (GABA) aminotransferase has been built based mainly on the structure of dialkylglycine decarboxylase and on a multiple sequence alignment of 28 evolutionarily related enzymes. The proposed active site structure is presented and analyzed. Hypothetical structures for external aldimine intermediates explain several characteristics of the enzyme. In the GABA external aldimine model, the pro-S proton at C4 of GABA, which abstracted in the 1,3-azaallylic rearrangement interconverting the aldimine and ketimine intermediates, is oriented perpendicular to the plane of the pyridoxal phosphate ring. Lys 329 is in close proximity and is probably the general base catalyst for the proton transfer reaction. The carboxylate group of GABA interacts with Arg 192 and Lys 203, which determine the specificity of the enzyme for monocarboxylic ω-amino acids such as GABA. In the proposed structure for the L-glutamate external aldimine, the α-carboxylate interacts with Arg 445. Glu 265 is proposed to interact with this same arginine in the GABA external aldimine, enabling the enzyme to act on ω-amino acids in one half-reaction and on α-amino acids in the other. The reactivities of inhibitors are well explained by the proposed active site structure. The R and S isomers of β-substituted phenyl and p-chlorophenyl GABA would bind in very different modes due to differential steric interactions, with the reactive S isomer leaving the orientation of the GABA moiety relatively unperturbed compared to that of the natural substrate. In our model, only the reactive S isomer of the mechanism based inhibitor vinyl-GABA, an effective anti-epileptic drug known clinically as Vigabatrin, would orient the scissile C4-H bond perpendicular to the coenzyme ring plane and present the proton to Lys 329, the proposed general base catalyst of the reaction. The R isomer would direct the vinyl group toward Lys 329 and the C4-H bond toward Arg 445. The active site model presented provides a basis for site-directed mutagenesis and drug design experiments.

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