Steric mapping of the L-methionine binding site of ATP:L-methionine S-adenosyltransferase

Three-dimensional steric mapping of the L-methionine binding site of mammalian (rat liver) ATP:L-methionine S-adenosyltransferase (EC 2.5.1.6) has been accomplished by computing the combined occupied volume of six inhibitory, conformationally rigid, amino acid analogues that have been shown in previous studies, which used an enzyme preparation of undetermined isozymic composition, to bind to the enzyme surface in competition with L-methionine. These six amino acids, all of which are derivatives of 1-aminocyclopentane-1-carboxylic acid, include (1R,2R,4S)-2-aminonorbornane-2-carboxylic acid, (1S,2S,4R)-2-aminonorbornane-2-carboxylic acid, (1R,2S,4S)-2-aminonorbornane-2-carboxylic acid, (1R,2R,4S)-2-amino-5,6-exo-trimethylenenorbornane-2-carboxylic acid, 7-aminonorbornane-7-carboxylic acid, and 9-aminofluorene-9-carboxylic acid. This has generated an 'enzyme-excluded' volume map, which defines that region of the active site known to be available for binding by substrates or inhibitors structurally related to L-methionine. Volume mapping of three conformationally rigid analogues which possess the minimal structural requirements for recognition, but nevertheless are inactive, has been carried out to determine their unique volume requirements that are not associated with the enzyme-excluded volume. These inactive amino acids are (1S,2R,4R)-2-aminonorbornane-2-carboxylic acid, (1R,2R,4S)-2-aminobicyclo[3.2.1]octane-2-carboxylic acid, and 2-aminoadamantane-2-carboxylic acid. Intersection of the unique volume segments of the three inactive analogues shows one region of unique volume overlap for all three molecules and defines an 'enzyme-essential' region, i.e., a region required by the enzyme itself and not available for ligand binding.