Diaminopimelate decarboxylase, LysA
InterPro Protein Domain record
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description
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<p>Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-, arginine- and related substrates can be classified into different familieson the basis of sequence similarity [<cite idref="PUB00003632"/>, <cite idref="PUB00001452"/>]. One of these families includesornithine decarboxylase (ODC), which catalyses the transformationof ornithine into putrescine; prokaryotic diaminopimelic acid decarboxylase(DAPDC), which catalyses the conversion of diaminopimelic acid into lysine,the final step of lysine biosynthesis; <taxon tax_id="322">Pseudomonas syringae pv. tabaci</taxon>protein, tabA, which is probably involved in tabtoxin biosynthesis andis similar to DAPDC; and bacterial and plant biosynthetic argininedecarboxylase (ADC), which catalyses the transformation of arginine into agmatine, the first step in putrescine synthesis from arginine.</p><p>Although these proteins, which are known collectively as group IVdecarboxylases [<cite idref="PUB00001452"/>], probably share a common evolutionary origin, theirlevels of sequence similarity are low, being confined to a few shortconserved regions. These conserved motifs suggest a common structuralarrangement for positioning of substrate and the cofactor pyridoxal5'-phosphate among bacterial DAP decarboxylases, eukaryotic ornithinedecarboxylases and arginine decarboxylases [<cite idref="PUB00006113"/>].</p>Two lysine biosynthesis pathways evolved separately in organisms, the diaminopimelic acid (DAP) and aminoadipic acid (AAA) pathways. The DAP pathway synthesizes L-lysine from aspartate and pyruvate, and diaminopimelic acid is an intermediate. This pathway is utilised by most bacteria, some archaea, some fungi, some algae, and plants. The AAA pathway synthesizes L-lysine from alpha-ketoglutarate and acetyl coenzyme A (acetyl-CoA), and alpha-aminoadipic acid is an intermediate. This pathway is utilised by most fungi, some algae, the bacterium Thermus thermophilus, and probably some archaea, such as Sulfolobus, Thermoproteus, and Pyrococcus. No organism is known to possess both pathways [<cite idref="PUB00055043"/>].<p>There four known variations of the DAP pathway in bacteria: the succinylase, acetylase, aminotransferase, and dehydrogenase pathways. These pathways share the steps converting L-aspartate to L-2,3,4,5- tetrahydrodipicolinate (THDPA), but the subsequent steps leading to the production of meso-diaminopimelate, the immediate precursor of L-lysine, are different [<cite idref="PUB00055043"/>].</p><ul><li>The succinylase pathway acylates THDPA with succinyl-CoA to generate N-succinyl-LL-2-amino-6-ketopimelate and forms meso-DAP by subsequent transamination, desuccinylation, and epimerization. This pathway is utilised by proteobacteria and many firmicutes and actinobacteria. </li><li>The acetylase pathway is analogous to the succinylase pathway but uses N-acetyl intermediates. This pathway is limited to certain Bacillus species, in which the corresponding genes have not been identified. </li><li>The aminotransferase pathway converts THDPA directly to LL-DAP by diaminopimelate aminotransferase (DapL) without acylation. This pathway is shared by cyanobacteria, Chlamydia, the archaeon Methanothermobacter thermautotrophicus, and the plant Arabidopsis thaliana. </li><li>The dehydrogenase pathway forms meso-DAP directly from THDPA, NADPH, and NH4 _ by using diaminopimelate dehydrogenase (Ddh). This pathway is utilised by some Bacillus and Brevibacterium species and Corynebacterium glutamicum. </li></ul><p>Most bacteria use only one of the four variants, although certain bacteria, such as C. glutamicum and Bacillus macerans, possess both the succinylase and dehydrogenase pathways.</p><p>This entry represents diaminopimelate decarboxylase, LysA, which converts meso-diaminopimelate into lysine and is the last step of the DAP lysine biosynthetic pathway. The structure of bacterial diaminopimelate decarboxylase has been determined [<cite idref="PUB00014556"/>].</p>
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Diaminopimelate decarboxylase, LysA
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InterPro Protein Domain record
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Os_RAPDB_Locus
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