Nicotinic acid hydroxylase (NAH) from Clostridium barkeri contains selenium in a non-identified form that can be released by different denaturation procedures as a small molecular weight compound. Some biochemical and EPR properties of the molybdopterin cofactor of NAH are quite different from those of other Mo-containing enzymes. Enrichment with Se-77 leads to 12 G splitting of the Mo(V) EPR signal of the native protein without affecting the iron signals of Fe-S clusters. This is direct evidence for coordination of Se with molybdenum. NAH isolated from cells grown in selenium-deficient media has no significant nicotinate hydroxylase activity or Mo(V) EPR signal; however, it has about the same NADPH oxidase and diaphorase activities, indicating that Se is present in a cofactor form that is essential for physiologically important catalytic activity. Denaturation procedures carried out in the anaerobic laboratory show that Se does not appear to be present as a terminal ligand of the molybdopterin cofactor. Xanthine dehydrogenase isolated from Clostridium purinolyticum is similar to NAH with regard to properties of selenium, suggesting that in both enzymes Se in a common cofactor is coordinated to Mo in the molybdopterin.