The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1

Mosaic Evolution of the Phosphopantothenate Biosynthesis Pathway in Bacteria and Archaea

Phosphopantothenate is a precursor to synthesis of coenzyme A, a molecule essential to many metabolic pathways. Organisms of the archaeal phyla were shown to utilize a different phosphopantothenate biosynthetic pathway from the eukaryotic and bacterial one. In this study, we report that symbiotic bacteria from the group Candidatus poribacteria present enzymes of the archaeal pathway, namely pantoate kinase and phosphopantothenate synthetase, mirroring what was demonstrated for Picrophilus torridus, an archaea partially utilizing the bacterial pathway. Our results not only support the ancient origin of the coenzyme A pathway in the three domains of life but also highlight its complex and dynamic evolution. Importantly, this study helps to improve protein annotation for this pathway in the C. poribacteria group and other related organisms.

Crystal structure of pantoate kinase from Thermococcus kodakarensis

The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4'-phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.

The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation

Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.

Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis

Bacteria/eukaryotes share a common pathway for coenzyme A biosynthesis which involves two enzymes to convert pantoate to 4'-phosphopantothenate. These two enzymes are absent in almost all archaea. Recently, it was reported that two novel enzymes, pantoate kinase, and phosphopantothenate synthetase (PPS), are responsible for this conversion in archaea. Here, we report the crystal structure of PPS from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complexes with substrates, ATP, and ATP and 4-phosphopantoate. PPS forms an asymmetric homodimer, in which two monomers composing a dimer, deviated from the exact twofold symmetry, displaying 4°-13° distortion. The structural features are consistent with the mutagenesis data and the results of biochemical experiments previously reported. Based on these structures, we discuss the catalytic mechanism by which PPS produces phosphopantoyl adenylate, which is thought to be a reaction intermediate.