Molybdenum and tungsten enzymes which contain the pyranopterin cofactor are ubiquitous in Nature and perform a wide variety of biological functions. They catalyze a diversity of mostly two-electron oxidation–reduction reactions crucial in the metabolism of nitrogen, sulfur and carbon. These enzymes share common structural features, but reveal different polypeptide folding topologies and different active site coordination geometries, which, in part, dictate their function and specificity. On the basis of structural, spectroscopic and biochemical characteristics, they have been classified into three broad families named according to well-studied enzymes of each family: xanthine oxidase, sulfite oxidase and DMSO reductase. An overview of the X-ray crystallography data for representative members of the three enzyme families is given here, focusing on the mechanistic implications drawn from the structural data.