Crystal structures of dialkylglycine decarboxylase inhibitor complexes.
The crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.
Malashkevich
V N
VN
Department of Structural Biology, Biozentrum University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland. malashkevich@wi.mit.edu
Strop
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P
Keller
J W
JW
Jansonius
J N
JN
Toney
M D
MD
D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry; D000598:Amino Acids, Cyclic; D002262:Carboxy-Lyases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D018360:Crystallography, X-Ray; D003523:Cycloserine / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D011188:Potassium / Q000737:chemistry; D011725:Pyridines / Q000737:chemistry; D011732:Pyridoxal Phosphate / Q000737:chemistry
C402504:5'-phosphopyridoxyl-2-methylalanine; D000596:Amino Acids; D000598:Amino Acids, Cyclic; D008024:Ligands; D011725:Pyridines; C023863:1-aminocyclopropane-1-carboxylic acid; D011732:Pyridoxal Phosphate; D003523:Cycloserine; D002262:Carboxy-Lyases; C063519:2,2-dialkylglycine decarboxylase; D000409:Alanine; D011188:Potassium