Amino acid-binding regulatory domains

Figure 24.23. A Recurring Regulatory Domain. The regulatory domain formed by two subunits of 3-phosphoglycerate dehydrogenase is structurally related to the single-chain regulatory domain of threonine deaminase. Sequence analyses have revealed this amino acid-binding regulatory domain to be present in other enzymes as well.

To interact with bases in the major groove of DNA, a protein requires a relatively small structure that can stably protrude from the protein surface. The DNA-binding domains of regulatory proteins tend to be small (60 to 90 amino acid residues), and the structural motifs within these domains that are actually in contact with the DNA are smaller still. Many small proteins are unstable because of their limited capacity to form layers of structure to bury hydrophobic groups (p. 118). The DNA-binding motifs provide either a very compact stable structure or a way of allowing a segment of protein to protrude from the protein surface. 

In addition to structural domains devoted to DNA binding and dimerization (or oligomerization), many regulatory proteins must interact with RNA polymerase, with unrelated regulatory proteins, or with both. At least three different types of additional domains for protein-protein interaction have been characterized (primarily in eukaryotes) glutamine-rich, proline-rich, and acidic domains, the names reflecting the amino acid residues that are especially abundant. 

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