A DIVERSE SUPERFAMILY OF ENZYMES WITH ATP-DEPENDENT CARBOXYLATE-AMINETHIOL LIGASE ACTIVITY/

The recently developed PSI-BLAST method for sequence database search a nd methods for motif analysis were used to define and expand a superfa mily of enzymes with an unusual nucleotide-binding fold, referred to a s palmate, or ATP-grasp fold. In addition to D-alanine-D-alanine ligas e, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, enzymes with known three-dimensional structures, the ATP- grasp domain is predicted in the ribosomal protein S6 modification enz yme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzyme s of purine biosynthesis. All these enzymes possess ATP-dependent carb oxylate-amine ligase activity, and their catalytic mechanisms are like ly to include acylphosphate intermediates. The ATF-grasp superfamily a lso includes succinate-CoA ligase (both ADP-forming and GDP-forming va riants), malate-CoA ligase, and ATP-citrate lyase, enzymes with a carb oxylate-thiol ligase activity, and several uncharacterized proteins. T hese findings significantly extend the variety of the substrates of AT P-grasp enzymes and the range of biochemical pathways in which they ar e involved, and demonstrate the complementarity between structural com parison and powerful methods for sequence analysis.