TY - JOUR
T1 - Structural and Mechanistic Analysis of Two Refined Crystal Structures of the Pyridoxal Phosphate-dependent Enzyme Dialkylglycine Decarboxylase
AU - Toney, Michael D.
AU - Hohenester, Erhard
AU - Keller, John W.
AU - Jansonius, Johan N.
PY - 1995/1/13
Y1 - 1995/1/13
N2 - Two refined structures, differing in alkali metal ion content, of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) are presented in detail. The enzyme is an α tetramer, built up as a dimer of dimers, with a subunit molecular mass of 46.5 kDa. The fold of DGD is similar to those of aspartate aminotransferase, ω-amino acid aminotransferease and tyrosine phenol-lyase. The structure has two binding sites for alkali metal ions. GDG with potassium in site 1 (near the active site) and sodium in site 2 (at the surface of the molecule) has been refined against 2.6Å resolution data (R-factor=17.6%), and DGD with sodium at both sites has been refined against 2.1 Å resolution data (R-factor=17.8%). The proximity of site 1 to the active site accounts for the dependence of enzyme activity on potassium ions, and the observed active site structural changes caused by ion exchange at this site explain the inhibition of activity by sodium. DGD catalyzes both the decarboxylation of dialkylglycine species and the transamination ofl-amino acids in its normal catalytic cycle. The active site structure of DGD is moderately homologous to that of aspartate aminotransferase, which catalyzes only transamination; both the differences and similarities provide mechanistic guidelines for the DGD-catalyzed reactions. Models of thel-isovaline andl-alanine external aldimine intermediates suggest mechanisms by which the decarboxylation and transamination reactions could be accomplished within the single active site. Decarboxylatio is proposed to be at least partially catalyzed by stereo-electronic activation of the Cα-carboxylate bond achieved by orienting this bond perpendicular to the plane of the pyridinium ring in the dialkylglycine external aldimine intermediate. Transamination is proposed to be catalyzed by a similar effect on the Cα-H bond of thel-amino acid external aldimine intermediate, combined with general base catalysis provided by Lys272, in analogy to the mechanism of as partate aminotransferase.
AB - Two refined structures, differing in alkali metal ion content, of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) are presented in detail. The enzyme is an α tetramer, built up as a dimer of dimers, with a subunit molecular mass of 46.5 kDa. The fold of DGD is similar to those of aspartate aminotransferase, ω-amino acid aminotransferease and tyrosine phenol-lyase. The structure has two binding sites for alkali metal ions. GDG with potassium in site 1 (near the active site) and sodium in site 2 (at the surface of the molecule) has been refined against 2.6Å resolution data (R-factor=17.6%), and DGD with sodium at both sites has been refined against 2.1 Å resolution data (R-factor=17.8%). The proximity of site 1 to the active site accounts for the dependence of enzyme activity on potassium ions, and the observed active site structural changes caused by ion exchange at this site explain the inhibition of activity by sodium. DGD catalyzes both the decarboxylation of dialkylglycine species and the transamination ofl-amino acids in its normal catalytic cycle. The active site structure of DGD is moderately homologous to that of aspartate aminotransferase, which catalyzes only transamination; both the differences and similarities provide mechanistic guidelines for the DGD-catalyzed reactions. Models of thel-isovaline andl-alanine external aldimine intermediates suggest mechanisms by which the decarboxylation and transamination reactions could be accomplished within the single active site. Decarboxylatio is proposed to be at least partially catalyzed by stereo-electronic activation of the Cα-carboxylate bond achieved by orienting this bond perpendicular to the plane of the pyridinium ring in the dialkylglycine external aldimine intermediate. Transamination is proposed to be catalyzed by a similar effect on the Cα-H bond of thel-amino acid external aldimine intermediate, combined with general base catalysis provided by Lys272, in analogy to the mechanism of as partate aminotransferase.
KW - alkalki metal ion binding sites
KW - dialkylglycine decarboxylase
KW - enzyme mechanism
KW - pyridoxal-5′-phosphate
KW - X-ray crystallography
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U2 - 10.1006/jmbi.1994.0014
DO - 10.1006/jmbi.1994.0014
M3 - Article
C2 - 7799433
AN - SCOPUS:0028885266
VL - 245
SP - 151
EP - 179
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
SN - 0022-2836
IS - 2
ER -