Construction similarity networks of the cupin protein stuctures coloured by metal ligand. Pairwise similarities for a non-redundant established of 183 constructions from the Pfam cupin clan (CL0029) have been calculated making use of TM-align [37]. Each node represents a composition. Nodes have been organized using the yfiles organic format of of Cytoscape model 3.. A. Edges among nodes ended up drawn only if the regular MCE Chemical Birinapant TM-rating ..53 for that edge. At this cutoff, the common r.m.s.d. is two.91 A with an common of 158. Ca atoms aligned. B. Edges between nodes were drawn only if the typical TMscore ..sixty five for that edge. At this cutoff, the average r.m.s.d. is 2.44 A with an typical of 185.four Ca atoms aligned. Construction similarity networks of cupin domains coloured by metal ligand. Pairwise similarities for a non-redundant set of 213 domains from the Pfam cupin clan (CL0029) have been calculated utilizing TM-align [37]. Every node signifies a domain. Nodes had been organized making use of the yfiles natural format of of Cytoscape version 3.. A. Edges among nodes ended up drawn only if the regular TM-rating ..fifty three for that edge. At this cutoff, the common r.m.s.d. is one.73 A with seventy four.2 Ca atoms aligned. B. Edges among nodes had been drawn only if the regular TM-score ..sixty five for that edge. At this cutoff, the common r.m.s.d. is one.forty two A with eighty.1 Caatoms aligned. Construction similarity networks coloured by species and purpose. This is the very same network as in 3B but colored according to A. species and B. purpose.
Sequence similarity networks coloured by steel ligand. Networks have been generated by all-by all BLAST comparisons of the 183 sequences corresponding to the unique cupin structures demonstrated in Determine three. Nodes have been organized utilizing the yfiles natural format of of Cytoscape variation 3.. A. Edges in between nodes are drawn only if the E-price is far better than of 1E-three.5. At this cutoff, edges at this threshold depict alignments with a median 32.1% identity over ninety three residues. B. Edges in between nodes are drawn only if the E-benefit is far better than of 1E-6..
The composition community at a a lot more permissive threshold (Determine 3A) obviously exhibits clustering correlated with purpose. For example, the four cysteine dioxygenases, which catalyzes the oxidation of the Lcysteine to its sulfinic acid by incorporating equally of the oxygen atoms from O2 into the product, are portion of a bigger cluster also that contains oxalate oxidase (OxOx) and auxin-binding protein at the decrease stringency (Determine 3A). In the a lot more stringent network (Determine 3B), the CDO buildings (Homo sapiens, PDB code: 2ic1 [47] Ralstonia eutropha, PDB code: 2gm6 Mus musculus PDB code: 2q4s [forty eight] and Pseudomonas aeruginosa PDB code: 3 uss) share first neighbor status with every other only and are related to the greater cluster through the putative CDO from Bacillus subtilis (PDB code: 3 eqe). These monocupins are represented in Figure 1E by the Mus musculus (mouse) enzyme. 18082228The metallic ion in this construction is Ni(II) and is coordinated by a few conserved residues (His 86, His88, and His140) as proven in Determine 2d. Biochemical characterization of this protein has proven that iron is necessary for catalytic action [sixteen]. CDOs cluster by purpose when the total buildings are when compared (Determine three), but continue to be separate thanks to the smaller sized location of alignment when when compared at the area amount at the same stringency (Determine 4, data not indicated with arrows). The majority of cupins for which there is structural data are from bacterial organisms. The CDOs cluster by function in the sequence networks (Determine six). These networks confirm and lengthen preceding observations that users of the cupin superfamily cluster by 
operate when the perform is described at a good stage, these kinds of as the oxidation of cysteine but do not do so when operate is described a lot more broadly [fifteen].
