Nomenclature of the Regulatory Subunit of Protein Kinase A

RI uses a CAP - like nomenclature convention. The 1-91 deletion mutant of RI is divided into three sections, cAMP binding domains A and B, and the short section at the N-terminal end of the protein before domain A begins.

For each section the beta sheets and strands are numbered and the alpha helices are denoted by capital letters that go in alphabetical order, corresponding to the sequential order of the helices. For each section the numbering and lettering starts over So, for example, the first helix in domain A is named A:A, while the second sheet in domain B would be named 2:B. The N-terminal section is denoted as N, but has a quirky naming conventions, as this is a deletion mutant with several residues that can't be seen in the pdb coordinates. Therefore and the helix present in the N sectionis named X:N.