Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ

Abstract

Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated–methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated–methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated–methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated–methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein–protein interaction interface in KRAS4b–PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.

Calmodulin and PI3K Signaling in KRAS Cancers

“…However, it is still unclear to what extent designing drugs to inhibit the interaction of K-Ras4B with PDEδ would accomplish this goal. The recent structure [82] coupled with earlier observations [83] and modeling suggest that PDEδ may be able to bind other depalmitoylated isoforms, and geranyl-geranylated K-Ras is also a PDEδ substrate; not only farnesylated K-Ras. CaM’s interaction with K-Ras4B and its role in KRAS -driven cancers have long been considered an option [5].…”

Interaction of KRas4b with anionic membranes: A special role for PIP 2

“…Full Length KRas4b was solvated and equilibrated for 20 ns using NAMD 2.11 molecular Dynamics software package [17] and was later found to be nearly identical to the recently published full-length structure of KRas4b. [18]…”

RAS Proteins and Their Regulators in Human Disease

“…Our structural work on full-length KRAS4b in complex with PDEδ showed that unlike Rho and Rab GDIs that interact with both prenylated lipid and switch regions of G-domain, PDEδ only interacts with the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b (Dharmaiah et al, 2016). Structure-based sequence analysis identified a 5-amino acid long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind to both farnesylated as well as geranylgeranylated KRAS4b.…”