cThe molecular basis for the ability of bacteria to live on caffeine as a sole carbon and nitrogen source is unknown. Pseudomonas putida CBB5, which grows on several purine alkaloids, metabolizes caffeine and related methylxanthines via sequential N-demethylation to xanthine. Metabolism of caffeine by CBB5 was previously attributed to one broad-specificity methylxanthine Ndemethylase composed of two subunits, NdmA and NdmB. Here, we report that NdmA and NdmB are actually two independent Rieske nonheme iron monooxygenases with N 1 -and N 3 -specific N-demethylation activity, respectively. Activity for both enzymes is dependent on electron transfer from NADH via a redox-center-dense Rieske reductase, NdmD. NdmD itself is a novel protein with one Rieske [2Fe-2S] cluster, one plant-type [2Fe-2S] cluster, and one flavin mononucleotide (FMN) per enzyme. All ndm genes are located in a 13.2-kb genomic DNA fragment which also contained a formaldehyde dehydrogenase. ndmA, ndmB, and ndmD were cloned as His 6 fusion genes, expressed in Escherichia coli, and purified using a Ni-NTA column. NdmA-His 6 plus His 6 -NdmD catalyzed N 1 -demethylation of caffeine, theophylline, paraxanthine, and 1-methylxanthine to theobromine, 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NdmB-His 6 plus His 6 -NdmD catalyzed N 3 -demethylation of theobromine, 3-methylxanthine, caffeine, and theophylline to 7-methylxanthine, xanthine, paraxanthine, and 1-methylxanthine, respectively. One formaldehyde was produced from each methyl group removed. Activity of an N 7 -specific N-demethylase, NdmC, has been confirmed biochemically. This is the first report of bacterial N-demethylase genes that enable bacteria to live on caffeine. These genes represent a new class of Rieske oxygenases and have the potential to produce biofuels, animal feed, and pharmaceuticals from coffee and tea waste.
Many natural products and xenobiotic compounds contain N-linked methyl groups. A search of the Combined Chemical Dictionary database (http://ccd.chemnetbase.com) identified 19,091 compounds out of approximately 500,000 entries that contain at least one N-methyl group. N-Demethylations of many of these compounds by members of cytochrome P450, flavoenzyme, and 2-ketoglutarate-dependent nonheme iron oxygenase families are critical biological processes in living organisms (1,12,17,27,31). These processes include detoxification of drugs and xenobiotic compounds, regulation of chromatin dynamics and gene transcription, and repair of alkylation damages in purine and pyrimidine bases in nucleic acids. Members of all aforementioned enzyme families also catalyze O-demethylation reactions (14). Bacteria have evolved highly specific Rieske [2Fe-2S] domaincontaining O-demethylases that belong to the Rieske oxygenase (RO) family for the degradation of methoxybenzoates (5, 16). However, to the best of our knowledge, there is no description of N-demethylation by ROs.Caffeine (1,3,7-trimethylxanthine) and related N-methylated xanthines are purine alkaloids that are ext...