The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families

Abstract

Background: Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates. Although PLP-dependent enzymes belong to a small number of independent evolutionary lineages, they encompass more than 160 distinct catalytic functions, thus representing a striking example of divergent evolution. The importance and remarkable versatility of these enzymes, as well as the difficulties in their functional classification, create a need for an integrated source of information about them.

Description: The B6 database http://bioinformatics.unipr.it/B6db contains documented B6-dependent activities and the relevant protein families, defined as monophyletic groups of sequences possessing the same enzymatic function. One or more families were associated to each of 121 PLP-dependent activities with known sequences. Hidden Markov models (HMMs) were built from family alignments and incorporated in the database. These HMMs can be used for the functional classification of PLP-dependent enzymes in genomic sets of predicted protein sequences. An example of such analyses (a census of human genes coding for PLP-dependent enzymes) is provided here, whereas many more are accessible through the database itself.

Conclusion: The B6 database is a curated repository of biochemical and molecular information about an important group of enzymes. This information is logically organized and available for computational analyses, providing a key resource for the identification, classification and comparative analysis of B6-dependent enzymes.

Figure 1

A schematic view of the different reaction types catalyzed by PLP-dependent enzymes that act on amino acids. In these enzymes, PLP is bound to the ε-amino group of a catalytic lysine residue, forming a Schiff base (internal aldimine). Covalent binding of the substrate amino acid occurs through a transimination reaction, leading to formation of an external aldimine intermediate (structure on the upper left corner). Subsequently, the protonated ring system of PLP acts as an electron sink, to stabilize species carrying a negative charge on the α-carbon (carbanions). Depending on the enzyme (and hence on the specific arrangement of the active site residues) such stabilized carbanions can be formed upon cleavage of any of the three covalent bonds connecting the α-carbon to its substituents. Removal of the carboxylate group is typical of decarboxylases. Removal of the amino acid side chain occurs for example in threonine aldolase. Finally, removal of the α-proton may be the prequel to the formation of various further intermediates, leading to racemization, cyclization, β- and γ-elimination, and transamination reactions [1,4,7].

Figure 2

The B6 database relational structure. This figure delineates the four modules composing the database and their relationships. The database of PLP-dependent enzyme families was assembled based on the examination of the literature and on a collection of functionally validated sequences, as described in the text. These families, and in particular the HMMs associated to them, have been used for the identification and functional classification of PLP-dependent enzymes in sets of predicted protein sequences from whole genomes.

Figure 3

Homology network of PLP-dependent enzymes. Nodes represent Hidden Markov models (HMMs) of PLP-dependent families. Edges represent homology connections (E < 10^-5) between families established by HMM-HMM comparisons [18]. Black edges connect protein families with the most significant similarities (E < 10^-50). The network is visualized with the "Degree sorted circle layout" of Cytoscape [19]. Colors were mapped into nodes using the structural group of the protein family as a node property.