Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold
Figure 7
The figures (A–D) show the quaternary structures of the proteins. N to C terminus of one chain of the dimeric proteins has been coloured as spectrum while the other as pink.
The ligands at the active site are shown as spheres. A. Ureidoglycolate hydrolase (1YQCa_), the reference protein, bound to the product. The fifty residues in the N terminus are involved in interaction with another subunit in the dimer through domain swapping. The region interacts with substrate in the other subunit. B. RmlC epimerase (1EPZa_) bound to the substrate. The region of large deviation with respect to 1YQCa_ corresponds to the strands forming a beta swapped dimer and covers the active site in the other subunit. C. Glucose-6-phosphate isomerase (1QXRa_) dimer bound to a substrate analog. The structurally variable region lies on the opposite face of the domain in contrast to the reference 1YQCa_ and forms the active site in the same domain. D. 5-keto-4-deoxyuronate isomerase (1XRU) is a dimeric bicupin with Zn bound at the active site. The functional domain considered for comparison lies at the C terminal end. The structurally different region lies at the active site but is not involved in domain swapping with the N terminal domain in the polypeptide.