From Protein Structure to Function with Bioinformatics.pdf

6 Function Diversity Within Folds and Superfamilies 161Figure 6.4 summarises the functional diversity in that superfamily, together withrepresentative structures for the main functional groups. Yet, due to the difficultyto apprehend function, it may well be that even within these extremely diversesuperfamilies, functional commonalities that are not apparent at this stage willcome to light as more data is collected and studied.6.3.3.2 Function Diversity Between Close HomologuesThe above sections described the amount of functional diversity that is to beexpected within protein superfamilies, with particular emphasis on remote homologues.But functional diversity is also observed between closer homologues (e.g.Fig. 6.4 Diversity of structures and functions in the HUP-domains superfamily (CATH code3.40.50.620). HUP-domains adopt a Rossmann-like fold and have been shown to be very ancient(Aravind et al. 2002). Together, they form a very large superfamily with many different functions.In this figure, representative structures of the major functional groups in this superfamily aredisplayed in cartoons. These structures were multiply aligned with CORA (Orengo 1999) and themultiple alignment was used to derive the common core of the domain. Residues that constitutethe core are coloured red in each structure. The CATH domains that were used as representativesof each functional groups are: (a) 1dnpA01 for DNA repair photolyases, (b) 1ej2A00 for nucleotidyltransferases,(c) 1gpmA02 for N-type ATP pyrophosphatases, (d) 1n3lA01 for class I aminoacyltRNA synthetases and (e) 1o97D01 for electron transfer flavoproteins