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IPR009006 is a Alanine racemase/group IV decarboxylase, C-terminal.
<p>This superfamily represents a β-barrel domain found at the C-terminal of alanine racemase ([ec:5.1.1.1]) and in group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases, such as eukaryotic ornithine decarboxylase ([ec:4.1.1.17]), arginine decarboxylase ([ec:4.1.1.19]) and diaminopimelate decarboxylase ([ec:4.1.1.20]). These enzymes belong to the same structural family [[cite:PUB00036036]].</p> <p>Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotic and eukaryotic proteins [[cite:PUB00006264], [cite:PUB00006317]]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A [[cite:PUB00000440]]. The alanine racemase monomer is composed of two domains, an eight-stranded α/β barrel at the N terminus, and a C-terminal domain essentially composed of β-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the α/β barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first β-strand of the α/β barrel.</p> <p>Eukaryotic ornithine decarboxylase (ODC) acts as a homodimer to produce putrescine (1,4-diaminobutane) from ornithine, where putrescine is the precursor of other polyamines in animals, plants, and bacteria. Arginine decarboxylase is also involved in putrescine biosynthesis. This is the first committed step in polyamine biosynthesis. Alanine racemase is a structurally homologous enzyme. Both proteins share a common α/β barrel that binds the cofactor via a Schiff base on the C-terminal end of the barrel [[cite:PUB00011776]].</p> <p>Diaminopimelate decarboxylase (DapDC) catalyses the final step of lysine biosynthesis in bacteria.</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Molecular function | Catalytic activity | Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Ornithine decarboxylase [Lotus japonicus] gi|34495197|emb|CAE02644.1| | 22 | ||
| – | Ornithine decarboxylase [Lotus japonicus] gi|34495197|emb|CAE02644.1| | 21 | ||
| – | Arginine decarboxylase [Lotus japonicus] gi|34495199|emb|CAE02645.1| | 24 | ||
| – | Arginine decarboxylase [Lotus japonicus] gi|34495199|emb|CAE02645.1| | 19 | ||
| – | PREDICTED: diaminopimelate decarboxylase 1, chloroplastic-like [Cicer arietinum] gi|502161433|ref|XP_004512163.1| | 23 | ||
| – | PREDICTED: diaminopimelate decarboxylase 1, chloroplastic-like [Cicer arietinum] gi|502161433|ref|XP_004512163.1| | 22 | ||
| – | PREDICTED: arginine decarboxylase-like [Cicer arietinum] gi|502149391|ref|XP_004507509.1| | 29 | ||
| – | Ornithine decarboxylase; TAIR: AT3G14390.1 Pyridoxal-dependent decarboxylase family protein; Swiss-Prot: sp|P50134|DCOR_DATST Ornithine decarboxylase; TrEMBL-Plants: tr|Q70KF6|Q70KF6_LOTJA Ornithine decarboxylase; Found in the gene: LotjaGi1g1v0432800 | 22 | ||
| – | Arginine decarboxylase; TAIR: AT4G34710.1 arginine decarboxylase 2; Swiss-Prot: sp|Q39827|SPE1_SOYBN Arginine decarboxylase; TrEMBL-Plants: tr|Q70KF5|Q70KF5_LOTJA Arginine decarboxylase; Found in the gene: LotjaGi1g1v0562700 | 22 | ||
| – | Diaminopimelate decarboxylase; TAIR: AT5G11880.1 Pyridoxal-dependent decarboxylase family protein; Swiss-Prot: sp|Q94A94|DCDA2_ARATH Diaminopimelate decarboxylase 2, chloroplastic; TrEMBL-Plants: tr|A0A151TUY1|A0A151TUY1_CAJCA Uncharacterized protein; Found in the gene: LotjaGi1g1v0690900 | 23 | ||
| – | Arginine decarboxylase; TAIR: AT2G16500.1 arginine decarboxylase 1; Swiss-Prot: sp|Q43075|SPE1_PEA Arginine decarboxylase; TrEMBL-Plants: tr|Q2PEQ1|Q2PEQ1_TRIPR Arginine decarboxylase; Found in the gene: LotjaGi3g1v0514900 | 28 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd06830 | CDD | 1 | 9.09 |