Molecular Architecture of the Mn2+-dependent Lactonase UlaG Reveals an RNase-like Metallo-β-lactamase Fold and a Novel Quaternary Structure

The ulaG gene, located in the ula regulon, is crucial for the catabolism of l-ascorbate under anaerobic conditions and it has been proposed to encode for the putative l-ascorbate-6-P lactonase. The ulaG gene is widespread among eubacteria, including human commensal and pathogenic genera such as Escherichia, Shigella, Klebsiella and Salmonella. Here, we report the three-dimensional structures of the apoenzyme and Mn2+ holoenzyme of UlaG from E. coli to 2.6 Å resolution, determined using single-wavelength anomalous diffraction phasing and molecular replacement, respectively. The structures reveal a highly specialized metallo-β-lactamase-like fold derived from an ancient structural template that was involved in RNA maturation and DNA repair. This fold has a novel quaternary architecture consisting of a hexameric ring formed by a trimer of UlaG dimers. A mononuclear Mn2+-binding site resides at the core of the active site, which displays micromolar affinity for Mn2+ and a distorted trigonal bipyramidal coordination. The active site Mn2+ ion can be replaced by Co2+ or Zn2+, but not by Fe3+. We further show that the Mn2+ or Co2+-loaded enzyme exhibits lactonase activity towards l-ascorbate 6-P, thereby providing the first direct evidence of its catalytic role in the l-ascorbate catabolic pathway. Guided by the structural homology, we show that UlaG is able to cleave phosphodiester linkages in cyclic nucleotides, suggesting that the conservation of the fold and of the key catalytic residues allows for the evolutionary acquisition of substrate specificity for novel but related substrates.