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EMBO reports 4, 9, 850–854 (2003)
doi:10.1038/sj.embor.embor914
A genomic overview of pyridoxal-phosphate-dependent enzymes
Riccardo Percudani & Alessio Peracchi
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Department of Biochemistry
and Molecular Biology, University of Parma, Parco Area delle Scienze
23/a, 43100 Parma, Italy
To whom correspondence should be addressed
Alessio Peracchi Tel: +39 521905137; Fax: +39 521905151;
peracchi@unipr.it
Received 23 April 2003; Accepted 16 June 2003; Published online 1 September 2003.
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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.
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