The chemokine superfamily consists of a large number of ligands and receptors. At first glance, this family appears redundant and their ligand-receptor relationships promiscuous, making its study challenging. However, analyzing this family from the evolutionary perspective greatly simplifies understanding both the organization and function of this apparently complex system. In particular, the f...

G protein-coupled receptors (GPCRs) mediate our sense of vision, smell, taste, and pain. They are also involved in cell recognition and communication processes, and hence have emerged as a prominent superfamily for drug targets. Unfortunately, the atomic-level structure is only available for rhodopsin family. We have recently developed first principles methods MembStruk and HierDock for predict...

Glycosyltransferases (GTs) are diverse enzymes organized into 65 families. X-ray crystallography and in silico studies have shown many of these to belong to two structural superfamilies: GT-A and GT-B. Through application of fold recognition and iterated sequence searches, we demonstrate that families 60, 62, and 64 may also be grouped into the GT-A fold superfamily. Analysis of conserved acidi...

The phospholipase D (PLD) superfamily is a diverse group of proteins that includes enzymes involved in phospholipid metabolism, a bacterial toxin, poxvirus envelope proteins, and bacterial nucleases. Based on sequence comparisons, we show here that the tyrosyl-DNA phosphodiesterase (Tdp1) that has been implicated in the repair of topoisomerase I covalent complexes with DNA contains two unusual ...

In vitro characterization experiments revealed the formations of 3-(trans-2’-aminocyclopropyl)alanine ((3-Acp)Ala) and 3-(trans-2’-nitrocyclopropyl)alanine ((3-Ncp)Ala) are originated via two homologous proteins, BelK HrmI, which regioselectively catalyze N?-oxygenation l-lysine. The enzymes belong to emerging heme-oxygenase-like diiron oxidase oxygenase (HDO) superfamily catalytic center is va...

Two new studies have shown how regulation of microtubule dynamics by members of the kinesin superfamily may guard against errors in spindle assembly and chromosome segregation.

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx super...