Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies
Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies
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DOI：
10.1093/molbev/msl133
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发表时间：
2007-01-01
影响因子：
10.7
通讯作者：
Salminen, Tiina A.
中科院分区：
文献类型：
--
作者：
Kidron, Heidi;Repo, Susanna;Salminen, Tiina A.
精氨酸脱羧酶（ADC）和鸟氨酸脱羧酶（ODC）参与腐胺的生物合成，腐胺是动物、植物和细菌中其他多胺的前体。这些吡哆醛-5 '-磷酸依赖性脱羧酶与二氨基庚二酸脱羧酶（DapDC）一起属于丙氨酸消旋酶（AR）结构家族，其催化细菌中赖氨酸生物合成的最后步骤。我们构建了AR结构家族中脱羧酶的多序列比对，并根据比对结果推断系统发育树。系统发育树由ADC、DapDC和ODC形成的3个不同的分支组成，这些分支从祖先脱羧酶分化而来。祖先的脱羧酶可能能够识别几种底物，在古细菌和细菌中，ODC可能保留了结合其他氨基酸的能力。以前，已经提出了ODC的一个参数来解释在哺乳动物细胞中检测到的ADC活性。根据我们的研究结果，这似乎不太可能，强调需要更加谨慎的功能分配使用序列数据和说明系统发育分析在澄清关系和推定的功能的持续价值。
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.