Crystal structure of B. subtilis YjcG characterizing the YjcG‐like group of 2H phosphoesterase superfamily

Abstract

The 2H phosphoesterase superfamily was first identified by Mazumder et al.1 This superfamily of enzymes shares a common catalytic site and preserves the activity of cyclic phosphodiesterase, although their protein sequences are extremely diversified. The superfamily was named after the two His residues from two conserved tetrapeptide motifs, HX(T/S)X (X, a hydrophobic residue), in the active site. Site-directed mutagenesis indicated that the two His residues were essential for the enzyme activity.2 The conserved two HX(T/S)X motifs is the typical characteristic of the superfamily. The superfamily of enzymes ubiquitously exists in almost all known species. They are even traceable to the last universal common ancestor (LUCA) of all known life forms involving in RNA metabolism, and have subsequently evolved to take several distinct biological roles.1 The 2H phosphoesterase superfamily has been classified into four major groups and a few divergent members. The four major groups include the archaeo-bacterial LigT-like group, the eukaryotic-viral LigT-like group, the YjcG-like group, and the mlr3352-like group.1 We have selected the Bacillus subtilis YjcG gene as one of the target genes due to its low homology to any structural known proteins during a structural genomics investigation at Peking University.3 Here we present the crystal structure of B. subtilis YjcG which is the archetype of the YjcG-like group. As the first three-dimensional structure of the group and the first 2H phosphoesterase from bacteria, it contributes to complete the structural landscape of the 2H phosphoesterase superfamily and would throw lights on the functional investigation of the YjcG-like group.