Purification and structural characterization of a novel pterin that is the immediate biosynthetic precursor for molybdopterin formation in Escherichia coli has been accomplished. The precursor is purified from acid extracts of cells of the Escherichia coli molybdopterin-deficient mutant chlN by reverse phase and ion exchange high performance liquid chromatography. Under a variety of conditions, this precursor oxidizes directly to the previously characterized pterin, compound Z (Johnson, J. L., Wuebbens, M. M., and Rajagopalan, K. V. (1989) J. Biol. Chem. 264, 13440-13447). Like, molybdopterin, the precursor is an oxygen-sensitive, 6-alkyl pterin with a 4-carbon phosphorylated side chain. Analysis by 31P NMR indicates that the precursor phosphate is bound in diester linkage to C-2' and C-4' of the side chain to form a 6-membered ring. The precursor does not contain either of the sulfurs present in molybdopterin, and reduction with sodium borohydride yields a C-1' hydroxyl function. Two-electron oxidation of the precursor results in stoichiometric production of the fully oxidized compound Z. Liquid chromatography-mass spectroscopy of the precursor yields an MH+ ion with a mass of 346, corresponding to a structure for the precursor which is a dihydro form of compound Z.