Pyruvate formate lyase is structurally homologous to type I ribonucleotidereductase

Background: Pyruvate formate lyase (PFL) catalyses a key step in Escherichi a coli anaerobic glycolysis by converting pyruvate and CoA to formate and a cetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvat e, involving an essential Ca radical of Gly734 and two cysteine residues, C ys418 and Cys419, which may form thiyl radicals required for catalysis. We undertook this study to understand the structural basis for catalysis. Results: The first structure of a fragment of PFL (residues 1-624) at 2.8 A ngstrom resolution shows an unusual barrel-like structure, with a catalytic beta finger carrying Cys418 and Cys419 inserted into the centre of the bar rel. Several residues near the active-site cysteines can be ascribed roles in the catalytic mechanism: Arg176 and Arg435 are positioned near Cys419 an d may bind pyruvate/formate and Trp333 partially buries Cys418. Both cystei ne residues are accessible to each other owing to their cis relationship at the tip of the beta finger. Finally, two clefts that may serve as binding sites for CoA and pyruvate have been identified. Conclusions: PFL has striking structural homology to the aerobic ribonucleo tide reductase (RNR): the superposition of PFL and RNR includes eight of th e ten strands in the unusual RNR cdp barrel as well as the beta finger, whi ch carries key catalytic residues in both enzymes. This provides the first structural proof that RNRs and PFLs are related by divergent evolution from a common ancestor.