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Fig. 5 | BMC Evolutionary Biology

Fig. 5

From: The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains

Fig. 5

Evolutionary relationships of Ephrin, cupredoxin and SRS superfamilies. a Schematic rendering showing a common β-sandwich structural fold shared between ancient cupredoxins (first two from left), ephrins (middle two) and the closely related SRS superfamily (last two). Homologous β-sheets forming the β-sandwich fold across families are highlighted in green (front) and brown (rear). The region of variability extending after strand-4 are highlighted in blue. The insert between the canonical strands-1 and 2 is highlighted in pink for s48/45 domain. The conserved cysteine at the top of strand-3 forming different cross-sheet disulphide bridges in ephrins and SRS families, as well as the cysteine that chelates the copper metal in cupredoxins are shown; red line denotes disulphide bridges. For more details, see Additional file 1, Figure S7. b Structure based sequence alignment of ephrin, monodomain cupredoxin and SRS superfamilies from diverse taxa. The alignment illustrates the homologous β-strands forming the common β-sandwich structural core across families. The alignment includes structural representatives of ephrins (green text), monodomain cupredoxins (brown text) and SRS superfamily (blue text). Aligned columns with > 40% consensus are highlighted in grey. The strands are mapped on top of the alignment based on (3CZU_B) and coloured same as panel A, while numbers are marked only for strands homologous across families. Cysteines forming disulphide linkages for ephrins are highlighted in blue and orange background, while for the SRS family in green. Residues involved in chelating copper in cupredoxins are highlighted in red, while the non-conservative substitutions at the structurally equivalent positions possibly resulting in the loss of copper binding ability in ephrins are highlighted in green. Copper chelating residues and numbers marked at the bottom of the alignment corresponds to 1JZG (Azurin) from Pseudomonas aeruginosa. Residues involved in the chelation of copper in monodomain cupredoxins (plastocyanin, azurin, rusticyanin) are shown as ball and stick model in the inset at the bottom of panel B. To view the full-length alignment including the loops connecting the strands, and all disulphide linkages refer to Additional file 1: Figure S8. c Phylogenetic relationships between ephrins, monodomain cupredoxins and SRS superfamily. Tree topology was inferred using maximum-likelihood approach in the IQ-TREE software and the support values were estimated using ultrafast bootstrap (percentage from 1000 replicates). The topology was also tested using maximum-likelihood approach implemented in FastTree and support values are shown in parentheses for major nodes. Bacterial monodomain cupredoxins were used as outgroup. See Additional file 1: Figure S9 for more detail on phylogeny and complete sequence labels and support values. Raw tree files are provided in Additional file 3

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