KRAS Switch Mutants D33E and A59G Crystallize in the State 1 Conformation

KRAS switch loop movements play a crucial role in regulating RAS signaling, and alteration of these sensitive dynamics is a principal mechanism through which disease-associated RAS mutations lead to aberrant RAS activation. Prior studies suggest that despite a high degree of sequence similarity, the switches in KRAS are more dynamic than those in HRAS. We determined X-ray crystal structures of the rare tumorigenic KRAS mutants KRAS^D33E, in switch 1 (SW1), and KRAS^A59G, in switch 2 (SW2), bound to GDP and found these adopt nearly identical, open SW1 conformations as well as altered SW2 conformations. KRAS^A59G bound to a GTP analogue crystallizes in the same conformation. This open conformation is consistent with the inactive “state 1” previously observed for HRAS bound to GTP. For KRAS^A59G, switch rearrangements may be regulated by increased flexibility in the ⁵⁷DXXGQ⁶¹ motif at codon 59. However, loss of interactions between side chains at codons 33 and 35 in the SW1 ³³DPT³⁵ motif drives changes for KRAS^D33E. The ³³DPT³⁵ motif is conserved for multiple members of the RAS subfamily but is not found in RAB, RHO, ARF, or Gα families, suggesting that dynamics mediated by this motif may be important for determining the selectivity of RAS–effector interactions. Biochemically, the consequence of altered switch dynamics is the same, showing impaired interaction with the guanine exchange factor SOS and loss of GAP-dependent GTPase activity. However, interactions with the RBD of RAF are preserved. Overall, these observations add to a body of evidence suggesting that HRAS and KRAS show meaningful differences in functionality stemming from differential protein dynamics independent of the hypervariable region.