A genomic overview of pyridoxal‐phosphate‐dependent enzymes

Abstract

Enzymes that use the cofactor pyridoxal phosphate (PLP) constitute a ubiquitous class of biocatalysts. Here, we analyse their variety and genomic distribution as an example of the current opportunities and challenges for the study of protein families. In many free‐living prokaryotes, almost 1.5% of all genes code for PLP‐dependent enzymes, but in higher eukaryotes the percentage is substantially lower, consistent with these catalysts being involved mainly in basic metabolism. Assigning the function of PLP‐dependent enzymes simply on the basis of sequence criteria is not straightforward because, as a consequence of their common mechanistic features, these enzymes have intricate evolutionary relationships. Thus, many genes for PLP‐dependent enzymes remain functionally unclassified, and several of them might encode undescribed catalytic activities. In addition, PLP‐dependent enzymes often show catalytic promiscuity (that is, a single enzyme catalyses different reactions), implying that an organism can have more PLP‐dependent activities than it has genes for PLP‐dependent enzymes. This observation presumably applies to many other classes of protein‐encoding genes.