A diverse superfamily of enzymes with ATP‐dependent carboxylate—amine/thiol ligase activity

Abstract The recently developed PSI‐BLAST method for sequence database search and methods for motif analysis were used to define and expand a superfamily of enzymes with an unusual nucleotide‐binding fold, referred to as palmate, or ATP‐grasp fold. In addition to d‐alanine‐d‐alanine ligase, 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 enzyme (RimK), urea amidolyase, tubulin‐tyrosine ligase, and three enzymes of purine biosynthesis. All these enzymes possess ATP‐dependent carboxylate‐amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates. The ATP‐grasp superfamily also includes succinate‐CoA ligase (both ADP‐forming and GDP‐forming variants), malate‐CoA ligase, and ATP‐citrate lyase, enzymes with a carboxylate‐thiol ligase activity, and several uncharacterized proteins. These findings significantly extend the variety of the substrates of ATP‐grasp enzymes and the range of biochemical pathways in which they are involved, and demonstrate the complementarity between structural comparison and powerful methods for sequence analysis.