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Collection : Elife (E-Journal - Via Crossref)

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Figure 5. BPPS-SIPRIS analysis of synaptojanin/EEP domains within INPP5 proteins. ; Color code: EEP-residues, yellow sidechains; INPP5 residues, red sidechains; INPP5B-, INPP5E- and SHIP2-subfamily residues, orange sidechains; ligands, cyan; atoms involved in hydrogen bonds, CPK coloring. (A). Human INPP5B in complex with phosphatidylinositol 3,4-bisphosphate (pdb: 4cml) (Trésaugues et al., 2014), which is associated with cytosolic and mitochondrial membranes (Speed et al., 1995). BPPS-SIPRIS results: EEP spherical cluster, p=5.8 × 10−13; INPP5 spherical cluster, p=3.9 × 10−7; INPP5B spherical cluster, p=0.0021. (B). INPP5 hydrogen bond network within human INPP5B (pdb: 3mtc) (unpublished). (C). View of INPP5-residues (in 3mtc) that bind the 4-phosphate group required for substrate recognition. (D). Human INPP5B with phosphate bound to a possible membrane interaction or allosteric site (Mills et al., 2016). (E). Human INPP5B Ocrl with glycerol bound to the same site as indicated in (D) (Trésaugues et al., 2014). (F). INPP5 subgroups within the BPPS-defined hierarchy. (G). Human INPP5E (pdb: 2xsw) (unpublished), which is associated with the primary cilium, an organelle involved in signal transduction (Jacoby et al., 2009) (spherical cluster, p=3.6 × 10−4). (H). Human SHIP2 (pdb: 4a9c) (Mills et al., 2012), which is associated with membrane ruffle formation (Hasegawa et al., 2011) (spherical cluster, p=0.30). The following source data are available for Figure 5.

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Figure 4. BPPS-SIPRIS analysis of synaptojanin/EEP domains. ; (A). The two major groups of the BPPS-defined EEP hierarchy examined here. (B). Human APE1 phosphorothioate substrate complex (pdb: 5dfi) (Freudenthal et al., 2015). Replacement of the phosphodiester bond with phosphorothioate prohibits cleavage by APE1 at the abasic site (circled). Cys310, which is nitrosated, is indicated. Color scheme: APE1 backbone trace, green; DNA strand containing the abasic site, cyan; complementary strand, marine blue; the BPPS-SIPRIS-defined residues distinctive of the EEP superfamily and of the exoIII-AP-endo family, yellow and red sidechains, respectively; basic residues within a loop interacting with the major groove of DNA, purple. (C). Close up of the APE1 active site. EEP-specific residues forming a hydrogen-bond network are shown with yellow sidechains. For clarity, only a few of the EEP- and exoIII-AP-endo-specific residues in the network are shown. The following source data are available for Figure 4.

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Figure 4—figure supplement 2. Maximum likelihood tree of an exonuclease-endonucease-phosphatase (EEP) domain-containing protein (A), an ATP-dependent endonuclease (B), a tyrosyl-DNA phosphodiesterase 2-like protein (C), and DNA mismatch repair (MutS-like) protein (D). ; Robust and complex corals are shown in brown and green text, respectively, and non-coral metazoan and choanoflagellate species are shown in blue text. Photosynthetic lineages, regardless of phylogenetic origin, are shown in magenta text and all other taxa are in black text. GenBank accession (GI) or other identifying numbers are shown for each sequence.

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