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

Humboldt-Universität zu Berlin, Berlín, Berlin, Germany
Journal of Biological Chemistry (Impact Factor: 4.57). 12/2001; 276(47):44108-16. DOI: 10.1074/jbc.M104759200
Source: PubMed

ABSTRACT The enzymatic catalysis of many biological processes of life is supported by the presence of cofactors and prosthetic groups originating from the common tetrapyrrole precursor uroporphyrinogen-III. Uroporphyrinogen-III decarboxylase catalyzes its conversion into coproporphyrinogen-III, leading in plants to chlorophyll and heme biosynthesis. Here we report the first crystal structure of a plant (Nicotiana tabacum) uroporphyrinogen-III 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 structural and modeling analyses of both enzymes allowed the proposal for a refined catalytic mechanism. Asp(82) and Tyr(159) seem to be the catalytic functional groups, whereas the other residues may serve in substrate recognition and binding, with Arg(32) steering its insertion. The crystallographic dimer appears to represent the protein dimer under physiological conditions. The dimeric arrangement offers a plausible mechanism at least for the first two (out of four) decarboxylation steps.

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    • "The proteins of photosynthesis and carbon assimilation are represented by the alpha subunit of ATP synthase (spots U7 and U15), that catalyzes ATP synthesis/hydrolysis coupled with a transmembrane H + -translocation in chloroplasts and mitochondria [25]; rubisco activase (spot D12), which promotes and maintains the catalytic activity of Rubisco [26]; and uroporphyrinogen decarboxylase (spot D13), which is located at the first branch point of the ubiquitous tetrapyrrole biosynthetic pathway. Decarboxylation of uroporphyrinogen leads to the biosynthesis of hemes and chlorophylls, whereas its C-methylation initiates the synthesis of vitamin B 12 , sirohemes, and the nickel-chelating cofactor F 430 [27]. Fig. 1. "
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    • "However, a dimeric structure was postulated in the case of chicken (Seki et al. 1986), humans (Whitby et al. 1998), and Nicotiana tabacum (Martins et al. 2001), suggesting that dimer formation would be a common property of the UroD protein family. In addition, a number of biochemical and structural studies propose the existence of a dimer-dependent catalysis (Martins et al. 2001). Species from the genus Chlorella are among the most widely distributed microalgae, and thus are found in phytoplankton from all kinds of environments. "
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