The Evolution of Function within the Nudix Superfamily

The Nudix superfamily encompasses over 80,000 protein domains from all
three domains of life. These proteins fall into four general functional
classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine
mismatch-specific adenine glycosylases (A/G-specific adenine
glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as
protein/protein interaction and transcriptional regulation. The largest
group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase
specificities. To understand the evolution of this vast number of
activities, we assembled and analyzed experimental and structural data for
205 Nudix proteins collected from the literature. We corrected erroneous
functions or provided more appropriate descriptions for 53 annotations
described in the Gene Ontology Annotation database in this family, and
propose 275 new experimentally-based annotations. We manually constructed
structure-guided sequence alignment of 78 Nudix proteins. Using the
structural alignment as a seed, we then made an alignment of 347 “select”
Nudix domains, curated from structurally determined, functionally
characterized, or phylogenetically important Nudix domains. Based on our
review of Nudix pyrophosphohydrolase structures and specificities, we
further analyzed a loop region downstream of the Nudix hydrolase motif
previously shown to contact the substrate molecule and possess known
functional motifs. This loop region provides a potential structural basis
for the functional radiation and evolution of substrate specificity within
the hydrolase family. Finally, phylogenetic analyses of the 347 select
protein domains and of the complete Nudix clan revealed general monophyly
with regard to function and a few instances of probable homoplasy.