Concentrations of GDP, which are expected to bind to the catalytic site and inhibit the autophosphorylation of succinyl-CoA synthetase (SCS) when NTP is used as a substrate, were found to increase the level of phosphoenzyme formed, The ability of GDP to do so is dependent upon the presence of a protein distinct from SCS. The effector protein could be separated from SCS by ammonium sulfate fractionation. Reconstitution experiments show that the protein inhibits SCS, that the inhibition is relieved by GDP, and that the inhibitor recognizes both Escherichia coli and eukaryotic forms of SCS. The inhibitor is itself regulated by the conditions used to grow the bacteria and in a manner that appears distinct from that of SCS. (C) 1997 Academic Press.