Pleckstrin homology (PH) domains and phosphoinositides

Abstract

PH (pleckstrin homology) domains represent the 11th most common domain in the human proteome. They are best known for their ability to bind phosphoinositides with high affinity and specificity, although it is now clear that less than 10% of all PH domains share this property. Cases in which PH domains bind specific phosphoinositides with high affinity are restricted to those phosphoinositides that have a pair of adjacent phosphates in their inositol headgroup. Those that do not [PtdIns3P, PtdIns5P and PtdIns(3,5)P2] are instead recognized by distinct classes of domains including FYVE domains, PX (phox homology) domains, PHD (plant homeodomain) fingers and the recently identified PROPPINs (b-propellers that bind polyphosphoinositides). Of the 90% of PH domains that do not bind strongly and specifically to phosphoinositides, few are well understood. One group of PH domains appears to bind both phosphoinositides (with little specificity) and Arf (ADP-ribosylation factor) family small G-proteins, and are targeted to the Golgi apparatus where both phosphoinositides and the relevant Arfs are both present. Here, the PH domains may function as coincidence detectors. A central challenge in understanding the majority of PH domains is to establish whether the very low affinity phosphoinositide binding reported in many cases has any functional relevance. For PH domains from dynamin and from Dbl family proteins, this weak binding does appear to be functionally important, although its precise mechanistic role is unclear. In many other cases, it is quite likely that alternative binding partners are more relevant, and that the observed PH domain homology represents conservation of structural fold rather than function.

Figure 1. Location of the binding site for two adjacent phosphate groups in the PLC-d1 and DAPP1 PH domains

Figures were generated using the coordinates of PLCδ-PH bound to Ins(1,4,5)P₃ [9] (left panel) and DAPP1-PH [13] bound to Ins(1,3,4,5)P₄ (middle panel) or with bound phosphates from the crystallization buffer (right panel). Each PH domain is in the same orientation, and the view is centered on the inositol phosphate binding site. Strands β1 and β2 of the PH domain are marked, as are the phosphate groups and the key basic side-chains involved in hydrogen bonding to the phosphates. The two vicinal phosphates that appear to be in a common location in these and all other high-affinity PH domains [34] are marked with asterisks. Note that the orientations of Ins(1,4,5)P₃ in the left panel and Ins(1,3,4,5)P₄ in the middle panel are related by a 180° rotation about an axis close to a line that can be drawn between the 1- and 4-phosphates. K30/R40 in PLCδ-PH and K173/R184 in DAPP1-PH are the key basic residues in the β1/β2 loop motif first identified by Skolnik and colleagues [36].

Figure 2. The disabled-1 (dab1) PTB domain bound simultaneously to PtdIns(4,5)P2 headgroup and an NPXY-containing peptide

Coordinates were from the structure determined by Stolt et al. [75]. This complex represents an example of how proteins and phosphoinositides may cooperate in driving membrane association of a PTB domain, and indeed PH domains such as those from the OSBP family. The gray oval marks the broad area in which phosphoinositides bind to the other PH domains discussed here.