3PFL

CRYSTAL STRUCTURE OF PFL FROM E.COLI IN COMPLEX WITH SUBSTRATE ANALOGUE OXAMATE

Summary for 3PFL

• Entry DOI: 10.2210/pdb3pfl/pdb
• Descriptor: PROTEIN (FORMATE ACETYLTRANSFERASE 1), OXAMIC ACID (3 entities in total)
• Functional Keywords: glycyl radical enzyme, transferase, glucose metabolism, lyase-transferase complex, lyase/transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P09373
• Total number of polymer chains: 2
• Total formula weight: 170833.90

Authors

Becker, A.,Fritz-Wolf, K.,Kabsch, W.,Knappe, J.,Schultz, S.,Wagner, A.F.V. (deposition date: 1999-05-14, release date: 2000-05-31, Last modification date: 2024-02-21)

Primary citation

Becker, A.,Fritz-Wolf, K.,Kabsch, W.,Knappe, J.,Schultz, S.,Volker Wagner, A.F.
Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase.
Nat.Struct.Biol., 6:969-975, 1999

PubMed Abstract: Pyruvate formate-lyase (PFL) from Escherichia coli uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419). We have determined by X-ray crystallography the structures of PFL (non-radical form), its complex with the substrate analog oxamate, and the C418A,C419A double mutant. The atomic model (a dimer of 759-residue monomers) comprises a 10-stranded beta/alpha barrel assembled in an antiparallel manner from two parallel five-stranded beta-sheets; this architecture resembles that of ribonucleotide reductases. Gly 734 and Cys 419, positioned at the tips of opposing hairpin loops, meet in the apolar barrel center (Calpha-Sgamma = 3.7 A). Oxamate fits into a compact pocket where C2 is juxtaposed with Cys 418Sgamma (3.3 A), which in turn is close to Cys 419Sgamma (3.7 A). Our model of the active site is suggestive of a snapshot of the catalytic cycle, when the pyruvate-carbonyl awaits attack by the Cys 418 thiyl radical. We propose a homolytic radical mechanism for PFL that involves Cys 418 and Cys 419 both as thiyl radicals, with distinct chemical functions.

PubMed: 10504733
DOI: 10.1038/13341

Experimental method

X-RAY DIFFRACTION (2.6 Å)