Solving the structure of the first protein kinase, the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), in 1991 launched a study that has continued now for over thirty years, and with computational tools and Cryo-EM we are still learning new things. That first structure lacked one key feature; no nucleotide was bound although ATP and Mg were in the crystallization buffer. The second structure in 1993 showed bound ATP with two Mg ions along with a high affinity pseudo-substrate inhibitor peptide (IP20), and this defined a novel ATP binding motif characterized by a glycine-rich loop (G-Loop) that was distinct from the classic P-Loop that is shared by GTPases, ATPases and metabolic kinases that work on small molecules. Although unappreciated at the time, the switch mechanism for this large family of enzymes that are so critical for biology was embedded in this motif. In 2009 McCammon with MD simulations captured the essence of that switch when he defined the second Mg ion as the “Lynchpin” for removal of ADP. This Mg ion is controlled by a conserved motif in the kinase domain referred to as the DFG motif, and positioning of this ion is driven by the assembly of a hydrophobic regulatory spine, which is the hallmark signature of every active kinase. The G-Loop and the “Lynchpin” Mg ion define the molecular switch mechanism that regulates every eukaryotic protein kinase, and the mechanism is functionally distinct from the P-Loop. The Leucine-rich repeat Kinase 2 (LRRK2) is a large macromolecular kinase, and mutations in LRRK2 cause it to be a major risk factor for Parkinson’s Disease. LRRK2 is one of few proteins that has both a kinase domain (G-Loop) and a GTPase domain (P-Loop) embedded in the same polypeptide chain. In LRRK2 we can observe crosstalk between these two important biological switches.

Deciphering a molecular switch

ACS Spring 2022

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