Many enzymes that require pyridoxal 5'-phosphate (PLP), a coenzyme from a vitamin B6, are involved in amino acid metabolism. B6 dependency syndromes are defined as a group of metabolic disorders which are prevented or alleviated by non-physiologically large doses of vitamin B6, and, hence, they are tacitly accounted for by some structural alteration in a responsible B6-dependent enzyme such as a decrease on the affinity for PLP as compared to the normal. In this article, the mode of binding the coenzyme is exemplified by the case of aspartate aminotransferase, a typical B6-dependent enzyme whose three-dimensional structure is known, and, several B6 dependency syndromes are briefly reviewed. Among these syndromes, the molecular basis of only gyrate atrophy has recently been defined by the identification of a mutation in the relevant enzyme, ornithine aminotransferase.