Structures of the Carbon-Phosphorus Lyase Complex Reveal the Binding Mode of the NBD-like PhnK

• Cryo-EM structures of a small, asymmetric C-P lyase complex at 7.8 Å resolution
• Only one PhnK binds to the dimeric core complex due to steric hindrance
• The NBD-like PhnK binds to a cytoplasmic protein, distinct from NBD-TMD interaction
• Binding of PhnK exposes the active site residue, Gly32 of PhnJ

SummaryThe carbon-phosphorus (C-P) lyase complex is essential for the metabolism of unactivated phosphonates to phosphate in bacteria. Using single-particle cryo-electron microscopy, we determined two structures of the C-P lyase core complex PhnG2H2I2J2, with or without PhnK. PhnG2H2I2J2 is a two-fold symmetric hetero-octamer. Its two PhnJ subunits provide two identical binding sites for PhnK. Only one PhnK binds to PhnG2H2I2J2 due to steric hindrance. PhnK is homologous to the nucleotide-binding domain (NBD) of ATP-binding cassette transporters. The α helices 3 and 4 of PhnK bind to α helix 6 and a loop (residues 227–230) of PhnJ, in a different mode from the binding of NBDs to their transmembrane partners. Moreover, binding of PhnK exposes the active site residue, Gly32 of PhnJ, located near the interface between PhnJ and PhnH. This structural information provides a basis for further deciphering of the reaction mechanism of the C-P lyase.