The activation loop of PIP5K functions as a membrane sensor essential for lipid substrate processing

Abstract

A nuclear magnetic resonance study reveals the molecular basis of activation and regulation of the lipid kinase PIP5K by membrane lipids.

Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

“…(A)]. The results from secondary structure analysis are in broad agreement with biochemical and nuclear magnetic NMR studies on activation loop of PIP5K …”

“…First, unlike the solved structures of PIP4K proteins, where the structure of the kinase domain activation loop was not determined, this region is now shown to contain an alpha helix, as predicted by secondary structure analysis. Recently, Liu et al have solved the structure of the activation loop of PIP5K using nuclear magnetic NMR studies and their results also show the formation of an amphipathic helix within the activation loop upon the interaction with the membrane . Second, the structure of the PIP5K protein from S. cerevisiae differed from its mammalian counterpart and from the structure of the PIP4K protein in the region where the 8 aa conserved insert is found in the yeast protein.…”

“…In the modeled structure of S. cerevisiae PIP5K, the 8 aa insert forms a positively-charged surface loop, which is present on the same face of the protein as the activation loop of the kinase domain, which based on earlier studies is implicated to play a role in the membrane binding of PIP5K. [24][25][26] To gain insights into the interactions between PIP5K and membrane, and the role of the 8 aa CSI in the PIP5K, we have carried out molecular dynamics (MD) simulations of S. cerevisiae PIP5K structure and different model lipid bilayer membranes. The MD simulation affords an important means for probing the dynamic behavior of interaction of peripheral membrane proteins with lipid bilayer environment.…”

Integrated regulation of the phosphatidylinositol cycle and phosphoinositide‐driven lipid transport at ER‐PM contact sites

“…The availability of the substrate also appears to be paramount, as PIP5Ks do not show the ability to bind zwitterionic or anionic membranes that lack PPIn lipids; although it is interesting to note that PtdOH has been identified as a potent coactivator of PIP5K catalytic activity . Coordination of the substrate by PIP5K appears to stem from a combination of the membrane sensing mechanism recently described for the extended activation loop in addition to inputs from the putative PIP‐binding motif . The most recent study, which utilizes the yeast cellular model to investigate the enzymology of a representative vertebrate PIP5K homolog from zebrafish ( Danio rerio ), now shows that the local PtdSer and cholesterol content of the PM are specific determinants that control the catalytic activity of PIP5K by influencing the membrane targeting of the activation loop .…”

Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P ₂ Synthesis

“…The substrate specificity and membrane targeting of PIP5Ks are determined by the specificity loop within their catalytic domains ( Figure 6A) (Fairn et al, 2009;Hu et al, 2015;Kunz et al, 2000). The specificity loop of PIP5K (5K loop ) folds into an amphipathic helix (AH) upon membrane binding ( Figures 6B and 6C) (Liu et al, 2016). We checked if an amphipathic property of the 5K loop is required for PIP5K function.…”