The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths - Fig 6

Details of the ligand migration paths identified in this study (A) and illustration of the surface at the re path in VAO, EUGO and PCMH (B). A: Crystal structures of VAO, EUGO and PCMH as well as selected frames from our simulations were aligned using PyMOL. Selected crystal structure residues (labelled with VAO numbering) are shown as sticks. Residues involved in the subunit interface path and their conformations in VAO are coloured in magenta. The conformations of the corresponding residues in EUGO and PCMH, are coloured in lighter or darker shades of magenta, respectively. Residues involved in the re path and their conformations in VAO are coloured in cyan. The conformations of the corresponding residues in EUGO and PCMH, are coloured in lighter or darker shade of cyan, respectively. Note that the loop carrying Tyr51 is completely absent in EUGO and PCMH and that Tyr408 present in VAO is a leucine in EUGO and PCMH. Selected residues from selected frames of our simulations are shown as lines, in grey. Frames showing the movement of Tyr51 and Tyr408 were taken from simulations with dioxygen, those showing movement of His466, Tyr503 and Met195 from simulations with phenolic ligands that were migrating through the subunit interface path. The respective other monomer of the three crystal structures is visible on the right of the figure as cartoon in red (cap domain) and green (FAD-binding domain). On the left, the cytochrome c subunit from PCMH is visible as cartoon, coloured in blue. B: Surface representation of the surface of the re path to illustrate the size of the channel leading to the re side of FAD in VAO, EUGO and PCMH. The proteins are shown as surfaces and the FAD cofactors as sticks, coloured in yellow. Note the different size of the channel in VAO and EUGO, as well as the blockage by the cytochrome c subunit in PCMH (blue mesh).