Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum - Implications for the catalytic mechanism

The enzymatic catalysis of many biological processes of life is supported b y the presence of cofactors; and prosthetic groups originating from the com mon tetrapyrrole precursor uroporphyrinogen-III. Uroporphyrinogen-III decar boxylase catalyzes its conversion into coproporphyrinogen-III, leading in p lants to chlorophyll and heme biosynthesis. Here we report the first crysta l structure of a plant (Nicotiana tabacum) uroporphyrinogen-M decarboxylase , together with the molecular modeling of substrate binding in tobacco and human enzymes. Its structural comparison with the homologous human protein reveals a similar catalytic cleft with six invariant polar residues, Arg(32 ), Arg(36), Asp(82), Ser(214) (Thr in Escherichia coli), Tyr(159), and His( 329) (tobacco numbering). The functional relationships obtained from the st ructural and modeling analyses of both enzymes allowed the proposal for a r efined catalytic mechanism. Asp(82) and Tyr(159) seem to be the catalytic f unctional groups, whereas the other residues may serve in substrate recogni tion and binding, with Arg(32) steering its insertion. The crystallographic dimer appears to represent the protein dimer under physiological condition s. The dimeric arrangement offers a plausible mechanism at least for the fi rst two (out of four) decarboxylation steps.