Caffeine is so common as a natural or added ingredient in beverages, food, and pharmaceuticals that its presence alone has been suggested as a valid marker for the presence of untreated human sewage in water sources and soils. Caffeine itself, as well as similar compounds called methylxanthines, can cause soil sterilization at high concentrations. Organisms like Pseudomonas putida produce enzymes capable of digesting caffeine and other methylxanthines. Their waste product, uric acid, enters natural cycles that break uric acid down to carbon dioxide and ammonium salts.
"Several bacterial strains capable of utilizing caffeine as sole growth substrate metabolize caffeine via N-demethylation...N-Demethylation of caffeine in bacteria results in production of either theobromine (3,7-dimethylxanthine) or paraxanthine (1,7-dimethylxanthine). Paraxanthine and theobromine are further N-demethylated to 7-methyl- xanthine and xanthine. Xanthine is subsequently oxidized to uric acid by xanthine oxidase/dehydrogenase, and the uric acid enters the normal purine catabolic pathway to form CO2 and NH4+." (Summers et al. 2011:584)
"Sequence analyses of the caffeine demethylase gene product...predicted both proteins to be Rieske [2Fe– 2S]-domain-containing non-haem iron oxygenases." (Summers et al. 2011:587)
"The N-demethylase component (Ndm) itself is a two-subunit enzyme with broad substrate specificity. It can remove N-methyl groups from caffeine, all three natural dimethylxanthines, 3-methylxanthine and 7-methylxanthine to produce xanthine." (Summers et al. 2011:588)
"P. [Pseudomonas] putida CBB5 uses a broad-specificity, two-component N-demethylase system to initiate biotransformation of caffeine and related natural purine alkaloids." (Summers et al. 2011:591)