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)-m ediated transamination reaction of L-alanine by the vitamin B6 coenzyme, sh ow that the Cu(II) complex of pyridoxal 5-phosphate-pyridoxamine 5-phosphat e (PLP-PMP) Schiff base (Cu . C16H18N3O10P2, 1) is spontaneously covalent-b onded between the azomethine carbons of two neighboring Schiff bases with t he (R,R)- or (S,S)-configuration, and is led to a dimer structure of the tr ans (2a) or cis (2b) conformational isomer around the covalent bond, depend ing 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. M olecular 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 P-z orbitals of the azomethine nitrogen and carbon atoms. Based on the transformation of 1 to 2a/2b, we propose a transition pathway via the aldim ine or ketimine dimer form concerning the metal- and PLP-catalyzed biomimed e transformation of amino acid.