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MBE Advance Access published online on September 22, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl133
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted September 18, 2006

Research Article

Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies

Heidi Kidron 1 *, Susanna Repo 1 *, Mark Johnson 1, and Tiina Salminen 1 *

1 Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku, Finland

* To whom correspondence should be addressed.
Tiina Salminen, E-mail: tsalmine{at}abo.fi


  Abstract

Arginine and ornithine decarboxylases are involved in the biosynthesis of putrescine, which is the precursor of other polyamines in animals, plants and bacteria. These pyridoxal 5'-phosphate dependent decarboxylases belong to the alanine racemase structural family together with diaminopimelate decarboxylase, which catalyzes the final step of lysine biosynthesis in bacteria. We have constructed a multiple sequence alignment of decarboxylases in the alanine racemase structural family and, based on the alignment, inferred phylogenetic trees. The phylogenetic tree consists of three distinct clades formed by arginine, diaminopimelate and ornithine decarboxylases that diverged from an ancestral decarboxylase. The ancestral decarboxylase probably was able to recognize several substrates and, in archaea and bacteria, ornithine decarboxylase may have retained the ability to bind other amino acids. Previously, a paralogue of ornithine decarboxylase has been proposed to account for arginine decarboxylase activity detected in mammalian cells. According to our results this appears unlikely, emphasizing the need for more caution in functional assignment made using sequence data and illustrating the continuing value of phylogenetic analysis in clarifying relationships and putative functions.

Keywords: decarboxylase; pyridoxal 5'-phosphate; evolution; phylogeny; protein structure.

*equal contribution


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