Figure 3.
Ddn Structures with and without Coenzyme F420
(A) Topology of split barrel-like fold oriented to the models. Arrows point to the post-β3 loop discussed in the text for orientation throughout the figure.
(B) Cartoon of Apo-1 structure showing split barrel-like fold.
(C) Cartoon of one monomer from Apo-1 (orange) aligned with one monomer from Apo-2 (purple) and showing Y130, Y133, Y136, and S78 for comparison. Y130 and Y136 are labeled.
(D) Cartoon of one monomer from the Holo-1 structure with F420 (magenta). The post-β3 loop (arrow) is repositioned to create the pocket for binding of the deazaflavin ring system. Key waters are shown as red spheres.
(E) Surface rendering of the pentameric structure from Holo-1 shows a complementary groove with positive (blue) charges near the negatively charged tail of F420. A small pocket is formed near the flavin ring system but is not enclosed by the protein monomers or pentamers. Although the biological relevance is unclear, the pentamer provides room for the missing N termini (center of ring or packed on the front face). The front face also packs against a second pentamer in both crystal forms, occluding the active sites or potentially allowing crosstalk between active sites.
(F) Cartoon of one monomer from Apo-1 (orange) aligned to one monomer from Holo-1 (cyan; F420 in magenta) and showing Y130, Y133, Y136, and S78 for comparison. See Table S2 for NMR characterization of NΔ30 Ddn with and without coenzyme.