Dihydropyrimidine dehydrogenase catalyzes, in the rate-limiting step of the pyrimidine degradation pathway, the NADPH-dependent reduction of uracil and thymine to dihydrouracil and dihydrothymine, respectively. The porcine enzyme is a homodimeric iron-sulfur flavoprotein (2 x 111 kDa). C671, the residue postulated to be in the uracil binding site and to act as the catalytically essential acidic residue of the enzyme oxidative half-reaction, was replaced by an alanyl residue. The mutant enzyme was overproduced in Escherichia coli DH5alpha cells, purified to homogeneity, and characterized in comparison with the wild-type species. An extinction coefficient of 74 mM-1 cm-1 was determined at 450 nm for the wild-type and mutant enzymes. Chemical analyses of the flavin, iron, and acid-labile sulfur content of the enzyme subunits revealed similar stoichiometries for wild-type and C671A dihydropyrimidine dehydrogenases. One FAD and one FMN per enzyme subunit were found. Approximately 16 iron atoms and 16 acid-labile sulfur atoms were found per wild-type and mutant enzyme subunit. The C671A dihydropyrimidine dehydrogenase mutant exhibited approximately 1% of the activity of the wild-type enzyme, thus preventing its steady-state kinetic analysis. Therefore, the ability of the C671A mutant and, for comparison, of the wild-type enzyme species to interact with reaction substrates, products, or their analogues were studied by absorption spectroscopy. Both enzyme forms did not react with sulfite. The wild-type and mutant enzymes were very similar to each other with respect to the spectral changes induced by binding of the reaction product NADP+ or of its nonreducible analogue 3-aminopyridine dinucleotide phosphate. Uracil also induced qualitatively and quantitatively similar absorbance changes in the visible region of the absorbance spectrum of the two enzyme forms. However, the calculated Kd of the enzyme-uracil complex was significantly higher for the C671A mutant (9.1 +/- 0.7 microM) than for the wild-type dihydropyrimidine dehydrogenase (0.7 +/- 0.09 microM). In line with these observations, the two enzyme forms behaved in a similar way when titrated anaerobically with a NADPH solution. Addition of an up to 10-fold excess of NADPH to both dihydropyrimidine dehydrogenase forms led to absorbance changes consistent with reduction of approximately 0.5 flavin per subunit, with no indication of reduction of the enzyme iron-sulfur clusters. Absorbance changes consistent with reduction of both enzyme flavins were obtained by removing NADP+ with a NADPH-regenerating system. On the contrary, the two enzyme species differed significantly with respect to their reactivity with dihydrouracil. Addition of dihydrouracil to the wild-type enzyme species, under anaerobic conditions, led to absorbance changes that could be interpreted to result from both partial flavin reduction and the formation of a complex between the enzyme and (dihydro)uracil. In contrast, only spectral changes consistent with formation of a complex between the oxidized enzyme and dihydrouracil were observed when a C671A mutant enzyme solution was titrated with this compound. Furthermore, enzyme-monitored turnover experiments were carried out anaerobically in the presence of a limiting amount of NADPH and excess uracil with the two enzyme forms in a stopped-flow apparatus. These experiments directly demonstrated that the substitution of an alanyl residue for C671 in dihydropyrimidine dehydrogenase specifically prevents enzyme-catalyzed reduction of uracil. Finally, sequence analysis of dihydropyrimidine dehydrogenase revealed that it exhibits a modular structure; the N-terminal region, similar to the beta subunit of bacterial glutamate synthases, is proposed to be responsible for NADPH binding and oxidation with reduction of the FAD cofactor of dihydropyrimidine dehydrogenase. The central region, similar to the FMN subunit of dihydroorotate dehydrogenases, is likely to harbor the site o