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MBE Advance Access originally published online on September 22, 2006
Molecular Biology and Evolution 2007 24(1):79-89; 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

Research Articles

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

Heidi Kidron1, Susanna Repo1, Mark S. Johnson and Tiina A. Salminen

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

E-mail: tiina.salminen{at}abo.fi.

Accepted for publication September 18, 2006.

Arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) 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 (AR) structural family together with diaminopimelate decarboxylase (DapDC), which catalyzes the final step of lysine biosynthesis in bacteria. We have constructed a multiple-sequence alignment of decarboxylases in the AR structural family and, based on the alignment, inferred phylogenetic trees. The phylogenetic tree consists of 3 distinct clades formed by ADC, DapDC, and ODC that diverged from an ancestral decarboxylase. The ancestral decarboxylase probably was able to recognize several substrates, and in archaea and bacteria, ODC may have retained the ability to bind other amino acids. Previously, a paralogue of ODC has been proposed to account for ADC 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.

Key Words: decarboxylase • pyridoxal-5'-phosphate • evolution • phylogeny • protein structure

1 These authors made equal contribution to this study.

Michele Vendruscolo, Associate Editor


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[Abstract] [Full Text] [PDF]


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