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 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.
Highlights
Enzymes that depend on vitamin B6 are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates
BMC Bioinformatics 2009, 10:273 http://www.biomedcentral.com/1471-2105/10/273 enzymes that act on amino acids include transamination, decarboxylation, racemization, and eliminations or replacements at the β- or γ-carbons
The database contains hidden Markov models (HMMs) that were built from family alignments and that can be employed for the identification and functional classification of pyridoxal 5'phosphate (PLP)-dependent enzymes in genomic sets of protein sequences
Summary
The increasing number of predicted protein sequences generated by genomic sequencing projects require methods to predict details regarding functions. The B6 database allows the comparison of newly sequenced PLP-dependent proteins with a curated collection of protein families, making it more reliable a preliminary functional classification and helping to pinpoint gene products that are the most interesting candidates to functional studies. Due to the progresses of functional genomics, as well as to classical biochemical and genetic approaches, the body of information on PLP-dependent enzymes is necessarily going to increase. AP collected the literature included in the database, selected the functionally validated sequences, helped to build the families, drafted and revised the man-. Both authors read and approved the final manuscript
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
