Fig. 2: Interchain interactions mediate nucleotide binding.

A (left) A single polypeptide chain (hereafter referred to simply as a “chain”) is comprised of the 3HB, NTD, and CAD. (middle) The CpaF hexamer consists of six chains mediated by interactions between the NTD of one chain and the CAD of an adjacent chain in a hand-to-shoulder configuration. (right) Packing units are defined as encompassing one full chain and the CAD of the adjacent chain. They are named according to their hexameric conformation and the bound nucleotide. Chains are labelled from a to f based on their positions within the hexamer. B–G Packing unit analyses for the compact and expanded structures. Packing units are numbered 1 to 3 according to their positions within an asymmetric unit of the hexamer. Full chains and their constituent domains are labelled from a to f and colored according to their bound nucleotides—ATP in purple, ADP in maroon, and Apo in gold. Atomic models of ATP in yellow and ADP in cyan are depicted in surface view while the residue R347 on the α9 helix in black is shown as a space-filling model colored by its side chain heteroatom. Active site analysis highlights residues, shown in stick representation, involved in stabilizing bound nucleotides. All residues and nucleotides are encased in their corresponding cryo-EM density (grey for amino acids, yellow for ATP, and cyan for ADP) contoured at the same threshold level within each dataset. Dotted blue lines denote hydrogen bonds. The side chain rotamers of R217, R223, and R347 are classified as “engaged”, “disengaged”, or “intermediate”. H Summary of whether the bound nucleotide is coordinated by R347 of the adjacent CAD for all the packing units of the two structures.