Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase

• Published in: Structure (London) Vol. 7; no. 7; pp. 733 - 744
• Main Authors: Leppänen, Veli-Matti, Merckel, Michael C, Ollis, David L, Wong, Kenny K, Kozarich, John W, Goldman, Adrian
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.07.1999
• Subjects: Acetyltransferases - chemistry; Amino Acid Sequence; Crystallography, X-Ray; enzyme mechanism; Models, Molecular; Molecular Sequence Data; Protein Conformation; pyruvate formate lyase; ribonucleotide reductase; Ribonucleotide Reductases - chemistry; structure; X-ray crystallography; X-ray crystallography; ribonucleotide reductase; pyruvate formate lyase; enzyme mechanism; structure
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(99)80098-7

Background: Pyruvate formate lyase (PFL) catalyses a key step in Escherichia coli anaerobic glycolysis by converting pyruvate and CoA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate, involving an essential C α radical of Gly734 and two cysteine residues, Cys418 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 2.8Å resolution shows an unusual barrel-like structure, with a catalytic β finger carrying Cys418 and Cys419 inserted into the centre of the barrel. Several residues near the active-site cysteines can be ascribed roles in the catalytic mechanism: Arg176 and Arg435 are positioned near Cys419 and may bind pyruvate/formate and Trp333 partially buries Cys418. Both cysteine residues are accessible to each other owing to their cis relationship at the tip of the β 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 ribonucleotide reductase (RNR): the superposition of PFL and RNR includes eight of the ten strands in the unusual RNR α/ β barrel as well as the β finger, which 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.