Probing the Nucleotide-Binding Site of Escherichia coli Succinyl-CoA Synthetase

Succinyl-CoA synthetase (SCS) catalyzes the reversible interchange of purine nucleoside diphosphate, succinyl-CoA, and Pi with purine nucleoside triphosphate, succinate, and CoA via a phosphorylated histidine (H246α) intermediate. Two potential nucleotide-binding sites were predicted in the β-subunit, and have been differentiated by photoaffinity labeling with 8-N3-ATP and by site-directed mutagenesis. It was demonstrated that 8-N3-ATP is a suitable analogue for probing the nucleotide-binding site of SCS. Two tryptic peptides from the N-terminal domain of the β-subunit were labeled with 8-N3-ATP. These corresponded to residues 107−119β and 121−146β, two regions lying along one side of an ATP-grasp fold. A mutant protein with changes on the opposite side of the fold (G53βV/R54βE) was unable to be phosphorylated using ATP or GTP, but could be phosphorylated by succinyl-CoA and Pi. A mutant protein designed to probe nucleotide specificity (P20βQ) had a Km(app) for GTP that was more than 5 times lower than that of wild-type SCS, whereas parameters for the other substrates remained unchanged. Mutations of residues in the C-terminal domain of the β-subunit designed to distrupt one loop of the Rossmann fold (I322βA, and R324βN/D326βA) had the greatest effect on the binding of succinate and CoA. They did not disrupt the phosphorylation of SCS with nucleotides. It was concluded that the nucleotide-binding site is located in the N-terminal domain of the β-subunit. This implies that there are two active sites ∼35 Å apart, and that the H246α loop moves between them during catalysis.