Carbamyl phosphate synthetase III, an evolutionary intermediate in the transition between glutamine-dependent and ammonia-dependent carbamyl phosphate synthetases.

The amino acid sequence of carbamyl phosphate synthetase (CPS) III from liver of spiny dogfish shark Squalus acanthias was deduced from the nucleotide sequence of its cDNA. Alignment of the derived amino acid sequence of CPS III with sequences of rat and frog CPS I and hamster CPS II reveals a high degree of amino acid identity, indicating that CPS III shares the same common ancestral genes as CPSs I and II. All of the CPSs examined show a high conservation of sequences in the adenine nucleotide binding domains and in residues that have been implicated in catalysis. The active-site cysteine residue required for glutamine-dependent activity by CPS II is preserved in the sequence of CPS III. Nevertheless, analysis of the protein sequences indicates that CPS III is more closely related to CPS I than to CPS II. The structure of CPS III, which is composed of a single polypeptide, is consistent with the view that CPS III evolved by fusion of separate genes coding for the glutaminase and synthetase domains of the enzyme and, like other CPSs, the synthetase domain evolved by duplication and fusion of an ancestral kinase gene. These results, together with the recent finding that frog CPS I retains the active site cysteine residue in the glutaminase domain required for glutamine-dependent activity, indicate that other amino acid substitutions critical for glutamine-dependent activity preceded loss of this catalytic cysteine residue. The results described here together with earlier biochemical evidence support the view that acetylglutamate and glutamine-dependent CPS III found in invertebrates and fish species represents an intermediate in the evolution of ancestral glutamine-dependent CPS II toward the acetylglutamate and ammonia-dependent CPS I of ureotelic terrestrial vertebrates.