Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis. May have a carrier function to deliver PLP to the target enzymes or a protective function so that PLP does not inactivate essential lysines in proteins (PubMed:26872910). Does not have amino acid racemase activity (PubMed:24097949). Monomer. During the stationary phase, the deletion mutant exhibits a completely different intracellular pool of amino acids and produces a significant amount of L-valine in the culture medium. The log-phase mutant displays slightly decreased coenzyme A levels, accumulates 2-ketobutyrate, 2-aminobutyrate, and, to a lesser extent, L-valine. Also exhibits an increase in the levels of isoleucine and valine metabolic enzymes (PubMed:24097949). The mutant also accumulates gamma-L-glutamyl-L-2-aminobutyryl-glycine (ophthalmic acid) (PubMed:27426274). The mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP), and is sensitive to an excess of pyridoxine but not of pyridoxal (PubMed:26872910). Most of the phenotypes observed in the absence of yggS are probably caused by lower activities of PLP-dependent enzymes (PubMed:26872910). Belongs to the pyridoxal phosphate-binding protein YggS/PROSC family.