The crystal structure of D-3-phosphoglycerate dehydrogenase reveals a limited number of contacts between the regulatory and substrate binding domains of each subunit in the tetrameric enzyme. These occur between the side chains of Arg-339, Arg-405, and Arg-107 in the regulatory domain and main chain carbonyls in the substrate binding domain. In addition, Arg-339 participates in a hydrogen bonding network within the regulatory domain involving Arg-338 and Tyr-410, the C-terminal residue of the enzyme subunit. Mutagenic analysis of these residues produce profound effects on the enzyme's sensitivity to serine, the cooperativity of serine inhibition, and in some cases, the apparent overall conformation of the enzyme. Mutations of Arg-405 and Arg-407, which span the interface where the two domains come together, reduce the cooperativity of inhibition and increase the sensitivity of the enzyme to serine concentration. Serine binding studies with Arg-407 converted to Ala demonstrate that cooperativity of serine binding is also significantly reduced in a manner similar to the reduction in the cooperativity of inhibition. Mutations of Tyr-410 and Arg-338 decrease the sensitivity to serine without an appreciable effect on the cooperativity of inhibition. In the case of Tyr-410, a deletion mutant demonstrates that this effect is due to the loss of the C-terminal carboxyl group rather than the tyrosine side chain. All mutations of Arg-339, with the exception of its conversion to Lys, had profound effects on the stability of the enzyme. In general, those mutants that decrease sensitivity to serine are those that participate mainly in intradomain interactions and may also directly affect the serine binding sites themselves. Those mutants that decrease cooperativity are those that participate in interdomain interaction within the subunit. The observation that the mutants that decrease cooperativity also increase sensitivity to serine suggests a potential separation of pathways between how the simple act of serine binding results in noncooperative active site inhibition in the first place and how serine binding also leads to cooperativity between sites in the native enzyme.