Structural comparison of the active site channels in rodent and primate vascular adhesion protein-1

In this study, we have made homology models of mouse, rat, and monkey vascular adhesion protein-1 (VAP-1) to reveal basis for the species-specific ligand recognition of VAP-1. Based on the structural comparisons, rodent VAP-1s have a narrower active site channel than primate VAP-1s. The variable residues in mouse and rat VAP-1, Phe447 from arm I and the polar residues from the first alpha-helix of the D3 domain together with C-terminal residues are likely to affect ligand recognition and binding.