Structure-guided phylogenetic reconstruction of the superfamily of
proteins sharing the metallo-β-lactamase fold
Abstract
The superfamily of metallo-β-lactamases (MBL) comprises an ancient group
of proteins found in all domains of life, sharing a characteristic αββα
fold and a histidine-rich motif for binding of transition metal ions,
with the ability to catalyze a variety of hydrolysis and redox
reactions. Herein, structural homology and sequence similarity network
(SSN) analysis are used to assist the phylogenetic reconstruction of the
MBL superfamily, introducing tanglegrams to evaluate structure-function
relationships. SSN neighborhood connectivity is applied for spotting
protein families within SSN clusters, showing that 98 % of the
superfamily remains to be explored experimentally. Further SSN research
is suggested in order to determine their topological properties, which
will be instrumental for the improvement of automated sequence
annotation methods.