Computed spatial homology between the L12 protein of chloroplast ribosome and 1.7 A structure of Escherichia coli L12 domain

A computer-graphic model of the tertiary structure of a functional domain in an organelle ribosomal protein was generated using the amino acid sequence of chloroplast ribosomal protein L12 from spinach (Bartsch, Kimura and Subramanian, Proc. Natl. Acad. Sci. USA 79, 6871-6875, 1982) and 1.7 A resolution coordinates of the E. coli L12 C-terminal fragment crystal (Leijonmarck, Eriksson and Liljas, Nature 286, 824-826, 1980). A comparison between the model and the experimentally derived structure shows that although 40% of the primary structure of this part of the two proteins has undergone amino acid replacements, the gross spatial structure of the domain is maintained and the character of the surfaces of possible functional importance are not significantly altered.     

Caffeine Junkie: an Unprecedented Glutathione S-Transferase-Dependent Oxygenase Required for Caffeine Degradation by Pseudomonas putida CBB5

Caffeine and other N-methylated xanthines are natural products found in many foods, beverages, and pharmaceuticals. Therefore, it is not surprising that bacteria have evolved to live on caffeine as a sole carbon and nitrogen source. The caffeine degradation pathway of Pseudomonas putida CBB5 utilizes an unprecedented glutathione-S-transferase-dependent Rieske oxygenase for demethylation of 7-methylxanthine to xanthine, the final step in caffeine N-demethylation. The gene coding this function is unusual, in that the iron-sulfur and non-heme iron domains that compose the normally functional Rieske oxygenase (RO) are encoded by separate proteins. The non-heme iron domain is located in the monooxygenase, ndmC, while the Rieske [2Fe-2S] domain is fused to the RO reductase gene, ndmD. This fusion, however, does not interfere with the interaction of the reductase with N₁- and N₃-demethylase RO oxygenases, which are involved in the initial reactions of caffeine degradation. We demonstrate that the N₇-demethylation reaction absolutely requires a unique, tightly bound protein complex composed of NdmC, NdmD, and NdmE, a novel glutathione-S-transferase (GST). NdmE is proposed to function as a noncatalytic subunit that serves a structural role in the complexation of the oxygenase (NdmC) and Rieske domains (NdmD). Genome analyses found this gene organization of a split RO and GST gene cluster to occur more broadly, implying a larger function for RO-GST protein partners.