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Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate

Nature Structural Biology volume 6, pages 182–190 (1999)Cite this article

Abstract

Oxidative decarboxylation of pyruvate to form acetyl–coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR). Thus, PFOR is a potential target for drug design against certain anaerobic pathogens. Here, we report the crystal structures of the homodimeric Desulfovibrio africanus PFOR (data to 2.3 Å resolution), and of its complex with pyruvate (3.0 Å resolution). The structures show that each subunit consists of seven domains, one of which affords protection against oxygen. The thiamin pyrophosphate (TPP) cofactor and the three [4Fe–4S] clusters are suitably arranged to provide a plausible electron transfer pathway. In addition, the PFOR–pyruvate complex structure shows the noncovalent fixation of the substrate before the catalytic reaction.

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Figure 1: Ribbon drawings of Desulfovibrio africanus PFOR, made with MOLSCRIPT48 and Raster3D49.
Figure 2: a, Stereoview, shown in the same orientation as Fig. 1a, of one subunit containing 1,231 residues, depicting the structural domains I–VII in different colors.
Figure 3: Ribbon drawings of the seven structural domains of Desulfovibrio africanus PFOR.
Figure 4: Structural comparison of PFOR to the homodimeric transketolase (TK) from baker's yeast22.
Figure 5: Stereo picture of cavities and channels in PFOR.
Figure 6: Binding of the TPP cofactor to PFOR.
Figure 7: Binding of pyruvate to the PFOR active site.

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Acknowledgements

We are indebted to N. Forget for her assistance in the purification of the enzyme and to R. Toci for growing the bacteria. We thank J.L. Ferrer (BM02) and A. Thompson (BM14) for help with data collection at European Synchrotron Radiation Facilities. The assistance of M. Roth in the collection and treatment of the MAD data is gratefully acknowledged. This study was supported by the CEA and the CNRS.

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  1. Laboratoire de Cristallographie et de Cristallogénèse des Protéines, Institut de Biologie Structurale J.–P. Ebel CEA–CNRS, 41 avenue des Martyrs, Grenoble, 38027, France

    Eric Chabrière, Marie–Helene Charon, Anne Volbeda & Juan–Carlos Fontecilla–Camps

  2. Unité de Bioénergétique et Ingénierie des Protéines, Institut de Biologie Structurale et Microbiologie CNRS, 31 chemin J. Aiguier, Marseille, 13402, France

    Laetitia Pieulle & Etienne Claude Hatchikian

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Correspondence to Marie–Helene Charon or Anne Volbeda.

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Chabrière, E., Charon, M., Volbeda, A. et al. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nat Struct Mol Biol 6, 182–190 (1999). https://doi.org/10.1038/5870

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