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.

Figure 1

Catalytic versatility of pyridoxal-phosphate-dependent enzymes. The Enzyme Commission (EC) identifies an enzyme activity using a four-digit number, where the first digit indicates the general class of the catalysed reaction (1, oxidoreductases; 2, transferases; 3, hydrolases; 4, lyases; 5, isomerases; 6, synthetases). Of six general classes, five include pyridoxal-phosphate (PLP)-dependent enzymes. The catalytic diversity within enzyme families and superfamilies can be illustrated by a set of concentric pie charts (Thornton et al., 2000). Here, we show the distribution of the 145 PLP-dependent activities that have been classified so far. Sectors are coloured according to EC classes. The circles, from inner to outer, represent the first, second, third and fourth levels in the EC hierarchy. The angle subtended by any segment is proportional to the number of activities it contains, making it clear that aminotransferases (EC 2.6.1) constitute the largest group of PLP-dependent enzymes. A list of the EC-classified PLP-dependent activities is provided in the supplementary information online. The structure of PLP is shown in the centre of the graph.

Figure 2

Distribution of genes that encode pyridoxal-phosphate-dependent enzymes in representative genomes. The organisms used as examples are: Mycoplasma genitalium (not a free-living organism), Methanococcus jannaschii, Sulfolobus solfataricus, Aeropyrum pernix, Pyrococcus abyssi, Clostridium perfringens, Staphylococcus aureus, Synechocystis sp. PCC 6803, Escherichia coli, Pseudomonas aeruginosa, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, Caenorhabditis elegans, Anopheles gambiae and Homo sapiens. (A) Total number of pyridoxal-phosphate (PLP)-dependent genes per genome; the fraction of sequences that could not be classified in terms of function, on the basis of our search criteria, is shown in red. The relatively high number of PLP-dependent genes in A. thaliana can be explained in part by the occurrence, for many enzymes, of at least three isoforms (cytoplasmic, mitochondrial and plastidic) that are encoded by different genes. (B) The percentage of genes in each genome that encode PLP-dependent enzymes. (C) The number of Enzyme Commission (EC)-classified PLP-dependent activities for which sequences were found in each genome. Note that similar numbers of activities can be found in organisms with very different assortments of enzymes. For example, only about one-third of the PLP-dependent activities found in E. coli are also found in H. sapiens, despite the fact that the two organisms have a similar absolute number of activities.

Alessio Peracchi & Riccardo Percudani. Alessio Peracchi is the recipient of an EMBO Young Investigator Award