Views of Structural Representatives from Six Families in the Kinase-Like Superfamily Other Than the TPKs

<p>Structures are shown in an open-face view, and using the same conventions as used for PKA in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>. ATP and metal ions are shown in mirror image where available in the structure. Similar to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>, secondary structural elements are colored according to their conservation status in the overall superfamily as follows: yellow, elements are part of the “universal core” seen in all kinases in the superfamily; orange, elements are present in more than two, but not all, of the kinases in the superfamily; red, elements shared between only two families; purple, elements seen only in this family, but inserted within in the portion of the chain forming the universal core; blue, elements seen only in this family, and connected to the N- or C-terminal ends of the universal core. Secondary structural elements are labeled according to the standard conventions for the individual structure. As in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>, the glycine-rich loop is rendered in green and the loop forming the linker region is rendered in red. For clarity, the conserved residues shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a> are not rendered in these structures, though in most cases they are similar. Structures shown are as follows: (A) aminoglycoside phosphotransferase (APH(3′)-IIIa [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b24" target="_blank">24</a>]); (B) CK (CKA-2 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b23" target="_blank">23</a>]); (C) ChaK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b20" target="_blank">20</a>]; (D) PI3K [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b21" target="_blank">21</a>]; (E) AFK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b22" target="_blank">22</a>]; and (F) PIPKIIβ [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b19" target="_blank">19</a>]. Molecular renderings in this figure were created with MOLSCRIPT [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90" target="_blank">90</a>].</p

Conventional Distance-Based Phylogenetic Tree of the Kinase-Like Superfamily, Based Only on the Sequence Alignment from Figure 3

<p>This tree did not explicitly incorporate structural information, and is provided for purposes of comparison with the Bayesian tree presented in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g004" target="_blank">Figure 4</a>. Structures are labeled by their PDB IDs, followed by the abbreviated name of the structure. The AKs are highlighted by orange ovals. Bootstrap values are provided for major branches. Some branches are too short for values to fit; these are marked with red letters that correspond to the following values: a, 199; b, 170; c, 101; d, 141. Branches highlighted in gray were not supported by bootstrap values above 500, and should be considered speculative (if based only on this tree data) [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b57" target="_blank">57</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b58" target="_blank">58</a>]. Many of the core relationships within the superfamily cannot be resolved with confidence using the conventional sequence-based approach.</p

Proposed Phylogeny for the Kinase-Like Superfamily, Based on a Unified Bayesian Analysis of Both the Sequence Alignment in Figure 3 and the Structural Character Matrix in Table 2

<p>Structures are labeled by their PDB IDs, followed by the abbreviated name of the structure. TPKs are to the left of the figure, and are labeled with their group membership. TPKs labeled with a black asterisk are classified differently in our tree compared with the classification produced by Manning et al<i>.</i> [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b07" target="_blank">7</a>]. The AKs are highlighted with an orange oval. Major branches are labeled with their posterior probabilities. Gray ovals represent areas of doubt in the tree, based on the tree itself and other aspects of our analysis (see text). The left-hand oval represents uncertainty as to the closest TPK relative to the AKs; it is unclear where precisely the AKs should link to the TPKs (note that this uncertainty does not include the branching of most of the TPK groups in this region, as these are generally well supported). The right-hand oval represents uncertainty as to the proper placement of ChaK and PIPKIIβ. These kinases are difficult to place with high confidence because of their extreme divergence. They are labeled with red asterisks to denote the speculative nature of the current placement (see text).</p

Enhanced Sequence Alignment Derived from the Structural Alignment of Kinase Representatives

<p>Enhanced Sequence Alignment Derived from the Structural Alignment of Kinase Representatives</p

Enhanced Sequence Alignment Derived from the Structural Alignment of Kinase Representatives

<p>Enhanced Sequence Alignment Derived from the Structural Alignment of Kinase Representatives</p

Shared Hydrogen-Bonding Networks between Distantly Related Structures in the Kinase-Like Superfamily

<p>Colors and nomenclature for secondary structural elements are identical to those provided in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g002" target="_blank">Figure 2</a>. Structures shown are the C-terminal subdomains of four structures: (A) PKA [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b70" target="_blank">70</a>]; (B) CKA-2 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b23" target="_blank">23</a>]; (C) PI3K [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b21" target="_blank">21</a>]; and (D) AFK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b22" target="_blank">22</a>]. For clarity, some portions of structures are omitted. Residues involved in the shared hydrogen-bond networks are shown in a ball-and-stick rendering. For clarity, side-chains are omitted for residues that only participate in the network via backbone interactions. Residues involved directly in catalysis or metal binding are shown with light-green stick regions in the ball-and-stick rendering. Metal atoms, when present, are shown as gray spheres. ATP (or ATP analog), when present, is shown in a line rendering. Hydrogen bonds are shown in cyan. The orientation of the structures is similar but not identical (structures were rotated somewhat to make H-bond contacts more visible). Molecular renderings in this figure were created with MOLSCRIPT [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90" target="_blank">90</a>].</p