Copper(II) Ion-Catalyzed and Molecular Packing-Dependent Dimerization of Pyridoxal 5-Phosphate–Pyridoxamine 5-Phosphate Schiff Base as a Structural Model for in Vitro Transformation of Amino Acid by Pyridoxal 5-Phosphate: X-Ray Crystal Structural Investigation

X-Ray crystal structures of the end products, obtained by in vitro Cu(II)-mediated transamination reaction of L-alanine by the vitamin B6 coenzyme, show that the Cu(II) complex of pyridoxal 5-phosphate–pyridoxamine 5-phosphate (PLP–PMP) Schiff base (Cu·C16H18N3O10P2, 1) is spontaneously covalent-bonded between the azomethine carbons of two neighboring Schiff bases with the (R,R)- or (S,S)-configuration, and is led to a dimer structure of the trans (2a) or cis (2b) conformational isomer around the covalent bond, depending on the molecular packing in the crystal. Since crystals of 1 have been obtained, the C–C covalent bond could be formed at the crystalline state. Molecular orbital calculations suggest that the electronic structure of the Schiff base is significantly delocalized by the coordination of the copper(II) ion; also the vertical stacking of 1 aromatic rings, which is suitable for the dimer formation, is promoted by electrostatic interactions between the Pz orbitals of the azomethine nitrogen and carbon atoms. Based on the transformation of 1 to 2a/2b, we propose a transition pathway via the aldimine or ketimine dimer form concerning the metal- and PLP-catalyzed biomimetic transformation of amino acid.