The selenocysteine Se-conjugates {RSe-Cys, or RSeCH2CH[(NH2)(COOH)]} metabolism catalyzed by pyridoxal 5'-phosphate (PLP)-dependent beta-lyases has been elucidated in the gas-phase at the density functional level. In this study, pyridoxal 5'-phosphate (PLP)-dependent beta-lyases has been modeled by the [(OMe)P(OH)(O)(2)](-) phosphate. It was shown that the reaction RSe-Cys --> RSeH + CH2C[(NH2)(COOH)], which is suggested to occur via the beta-H elimination, is energetically unfavorable and encounters high activation barriers of 54.0 (54.1), 54.6 (54.6), and 50.7 (50.9) kcal/mol for R = H, Me. and Ph, respectively. The participation of pyridoxal 5'-phosphate (PLP)-dependent beta-lyases significantly facilitates this reaction, and reduces the C-3-H-2 (or C-beta-W-beta) activation barrier by almost three times, from 50.7 (50.9) kcal/mol to 18.0 (18.1) kcal/mol for R = Ph. Amazingly, the presence of enzyme completely changes the suggested mechanism of the metabolism of selenocysteine Se-conjugates: In the absence of beta-lyases the reaction (in general) occurs via the direct beta-H-transfer mechanism, whereas with the participation of enzyme it may occur via the indirect beta-H-transfer mechanism called the "H-atom relay" mechanism which includes: (a) the P-H atom uptake by enzyme from the RSe-Cys and (b) the delivery of another H atom from the phosphate cofactor to the Se center.