plosone-phylo
Figure 4
Domain structure, phylogeny and conservation of critical catalytic features of ciliate PIPKs.A, Domain structure of Tetrahymena PIPKs. The RING domain predicted in PIPK2b and transmembrane and SecY domains in PIPK5 have been removed (see Table S1 and Methods). Domain boundaries, e-values and further details are given in Table S1. B, Unrooted neighbor-joining tree of catalytic domains from 37 ciliate PIPKs. Bootstrap values from 5000 replicates higher than 60% are indicated near the corresponding branches. Group 1, 2, 3 and 4 PIPKs are color coded (blue, green, red and purple respectively). Circles and triangles represent Tetrahymena and Paramecium PIPKs, respectively. Bar indicates number of amino acid substitutions per site. Phylogenetic relationships of ciliate group 2 PIPK genes were less resolved with less nodes supported by high bootstrap values. In Paramecium, 4 additional group 3 PIPKs that are organized in 2 pairs of paralogs (PtPIPK3c,d and PtPIPK3e,f) and they are most related to TtPIPK3 are not shown. C, Sequence alignment of the catalytic kinase domains from ciliate PIPKs and mammalian PIPKI? and PIPKII?. The position of prominent catalytic features is indicated by arrows and arrowheads and numbered residues refer to the mouse PIPKII? structure described in reference 46. Polygons indicate residues that interact with ATP or the phosphoinositide substrate (PtdIns5P) in the crystal structure of PIPKII? and they are conserved in both type I and II PIPKs [46]. The variable inserts between the MDYSL and IID motifs present in all PIPKs have been omitted. The residues K150, D278 and D369, essential for catalytic activity, are conserved in all but 2 Tetrahymena PIPKs (highlighted in grey; see text and Figure S4 for details). The DLKGS motif in TtPIPK2c (highlighted in grey) has been reconstituted from RNA sequencing data (Table S1). The position of the KKxE/AxxxK motif in the specificity loop is indicated by a bar; further K residues that may contribute are highlighted by light blue and most ciliate PIPK1, but not PIPK2, genes confront to the consensus KK motif. Note that in all but 2 ciliate PIPKs the +2 position (E/A residues) in the specificity loop is occupied by a Glu residue as in all PtdInsP 5-kinases.
Figure 4
Domain structure, phylogeny and conservation of critical catalytic features of ciliate PIPKs.A, Domain structure of Tetrahymena PIPKs. The RING domain predicted in PIPK2b and transmembrane and SecY domains in PIPK5 have been removed (see Table S1 and Methods). Domain boundaries, e-values and further details are given in Table S1. B, Unrooted neighbor-joining tree of catalytic domains from 37 ciliate PIPKs. Bootstrap values from 5000 replicates higher than 60% are indicated near the corresponding branches. Group 1, 2, 3 and 4 PIPKs are color coded (blue, green, red and purple respectively). Circles and triangles represent Tetrahymena and Paramecium PIPKs, respectively. Bar indicates number of amino acid substitutions per site. Phylogenetic relationships of ciliate group 2 PIPK genes were less resolved with less nodes supported by high bootstrap values. In Paramecium, 4 additional group 3 PIPKs that are organized in 2 pairs of paralogs (PtPIPK3c,d and PtPIPK3e,f) and they are most related to TtPIPK3 are not shown. C, Sequence alignment of the catalytic kinase domains from ciliate PIPKs and mammalian PIPKI? and PIPKII?. The position of prominent catalytic features is indicated by arrows and arrowheads and numbered residues refer to the mouse PIPKII? structure described in reference 46. Polygons indicate residues that interact with ATP or the phosphoinositide substrate (PtdIns5P) in the crystal structure of PIPKII? and they are conserved in both type I and II PIPKs [46]. The variable inserts between the MDYSL and IID motifs present in all PIPKs have been omitted. The residues K150, D278 and D369, essential for catalytic activity, are conserved in all but 2 Tetrahymena PIPKs (highlighted in grey; see text and Figure S4 for details). The DLKGS motif in TtPIPK2c (highlighted in grey) has been reconstituted from RNA sequencing data (Table S1). The position of the KKxE/AxxxK motif in the specificity loop is indicated by a bar; further K residues that may contribute are highlighted by light blue and most ciliate PIPK1, but not PIPK2, genes confront to the consensus KK motif. Note that in all but 2 ciliate PIPKs the +2 position (E/A residues) in the specificity loop is occupied by a Glu residue as in all PtdInsP 5-kinases.