A genomic overview of pyridoxal-phosphate-dependent enzymes.
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.
Percudani
Riccardo
R
Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze 23/a, 43100 Parma, Italy.
Peracchi
Alessio
A
D000818:Animals; D004798:Enzymes / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D011732:Pyridoxal Phosphate / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
D004798:Enzymes; D011732:Pyridoxal Phosphate