cGMP-dependent protein kinase 2 (PRKG2 encoded)

cGMP-dependent protein kinase 2 is a multidomain protein. At the C-terminal end is the AGC Group kinase domain (453 onwards). This acts on proteins (target) and ATP binds in the 459 – 467 pocket. As the protein name suggests the protein kinase activity is triggered by a modulating domain. Specifically, activation happens when cAMP/cGMP (its activator) binds in the regulatory domain. The C-terminal carboxyl is located between these two.

p.Asp761Glufs*34

• wild type
• mutant (extension)
• overlay

Whereas in most protein the C-terminal extension is tolerant to extensions (in E. coli 90% of the proteome), this is unlikely to be the case here as it plays a structural role. And three factors are against it:

• F762L is deleterious (+6 kcal/mol, overlay)
• Extension causes extensive clashes
• Extension is between the active site and the regulatory domain

Specifically, the C-terminus of the protein ends in a turn (759-762) and a phenylalanine (F762) whose sidechain and carboxyl are structural. The backbone carboxylate of the C-terminal residue, F762, hydrogen bonds with the hydroxyl of a threonine. As a result of any extension this interaction is lost. Changing the F762 to a leucine is deleterious (+6 kcal/mol) per se as it is a core residue and leucine is smaller. The subsequent residues cause extensive clashes. An amide C-terminal cap causes an extra +4 kcal/mol destabilisation, while subsequent insertions are much more deleterious. A bulky side chain of the first new residue (extra +6 kcal/mol) and even worse the side chain of the second (additional +17 kcal/mol), resulting in further disruption of the F762L cavity. These residues can only make a turn to fit despite their bulkiness. Hypothetically speaking, were these changes not deleterious and if the extension were to have no effect on catalysis from the domain point of view (extremely unlikely given the disruption), the conformational change (unknown) triggered by the regulatory domain is undoubtably abrogated due to the presence of a helix in the way.

Methods

The C-terminal domain of the structure is modelled primarily against PDB:5DYK, while the two other domains are the structures PDB:5C6C and PDB:5BV6. For methodological details (including code and models) see GitHub repo