Structural Basis for Endosomal Targeting by FYVE Domains

Abstract

The FYVE domain is a conserved protein motif characterized by its ability to bind with high affinity and specificity to phosphatidylinositol 3-phosphate (PI(3)P), a phosphoinositide highly enriched in early endosomes. The PI(3)P polar head group contacts specific amino acid residues that are conserved among FYVE domains. Despite full conservation of these residues, the ability of different FYVE domains to bind to endosomes in cells is highly variable. Here we show that the endosomal localization in intact cells absolutely requires structural features intrinsic to the FYVE domain in addition to the PI(3)P binding pocket. These features are involved in FYVE domain dimerization and in interaction with the membrane bilayer. These interactions, which are determined by non-conserved residues, are likely to be essential for the temporal and spatial control of protein associations at the membrane-cytosol interface within the endocytic pathway.The FYVE domain is a double zinc finger named after the first four proteins found to contain this motif (Fab1, YotB, Vac1p, and EEA1) (1). FYVE domains bind with high specificity to phosphatidylinositol 3-phosphate (PI(3)P) 1 (2-5), which is highly enriched in early endosomes (3). Crystallographic and NMR analyses of isolated FYVE domains and crystallographic analysis of the homodimeric C terminus of EEA1 (6 -10) have revealed that six residues from the FYVE domain directly contact the Ins(1,3)P 2 group. These residues are localized within three conserved signature motifs, the WXXD, R(R/K)H-HCR, and RVC motifs.Although FYVE domains bind PI(3)P efficiently in vitro, when expressed in cells, isolated FYVE domains often fail to localize to endosomes (11)(12)(13)(14). Observations such as these have suggested that the ability of FYVE domains to localize to early endosomes may be determined by structural features distinct from those directly involved in PI(3)P binding (10). However, there is very little sequence conservation among FYVE domains in regions that do not directly contact the Ins(1,3)P 2 group. Thus, the molecular basis for the differing ability of FYVE domains to localize to endosomes remains unknown.To resolve this question, we have systematically analyzed the cellular localization of a series of isolated FYVE domains from the mammalian proteins EEA1, Hrs, SARA, FGD1, and frabin. Beyond the FYVE domain, there are no functional or structural similarities among these proteins, and they each have been hypothesized to fulfill distinct cellular functions (13,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30).With the exception of one residue in the FYVE domain of FGD1, all these FYVE domains contain the specific residues that directly contact PI(3)P, and all bind to PI(3)P in vitro. However, as shown here, the ability of these domains to interact with endosomes when expressed in intact cells varies greatly. A comparative analysis of the structural features within these FYVE domains that correlate with in vivo endosome binding reveals a crucial role for two variable...

ESCRT-0 Assembles as a Heterotetrameric Complex on Membranes and Binds Multiple Ubiquitinylated Cargoes Simultaneously

“…Additionally, these data indicate that in the absence of STAM, Hrs exists a dimer that is capable of maintaining sufficient ESCRT-0 function for C. elegans viability. This finding is supported by previous work showing that the Hrs FYVE domain can undergo dimerization, leading to a higher affinity for PI3P in the endosomal membrane (35,36).…”

Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a β-propeller protein family

“…Remarkably, most FYVE domains must dimerize for efficient binding to endosomes to allow coordinated binding of two PtdIns3P molecules within the same membrane (40)(41)(42)(43). This suggests that for normal membrane association of these proteins, the affinity of a single phosphoinositide binding site might not be sufficient.…”

A phosphoinositide conversion mechanism for exit from endosomes

“…This blocks accessibility of PI(3)P for PI(3)P-dependent motor proteins and PI(3)P metabolizing enzymes (Petiot, Faure et al 2003). To allow dissociation of the FYVE-probe from endosomes, a single FYVE domain under a weak promoter (Hayakawa, Hayes et al 2004;Stuffers, Malerod et al 2010) or knockin of the GFP-tagged FYVE domain using CRISPR/ Cas9 technology within a genomic safe harbour locus (Doudna and Charpentier 2014) should be used. Thus, it would match binding constants of endogenous…”