InterPro domain: IPR009006

This superfamily represents a beta-barrel domain found at the C-terminal of alanine racemase ( 5.1.1.1 ) and in group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases, such as eukaryotic ornithine decarboxylase ( 4.1.1.17 ), arginine decarboxylase ( 4.1.1.19 ) and diaminopimelate decarboxylase ( 4.1.1.20 ). These enzymes belong to the same structural family [ 1 ].

Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [ 2 , 3 ]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A [ 4 ]. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel.

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 alpha/beta barrel that binds the cofactor via a Schiff base on the C-terminal end of the barrel [ 5 ].

Diaminopimelate decarboxylase (DapDC) catalyzes the final step of lysine biosynthesis in bacteria.

1. Functional classification of amino acid decarboxylases from the alanine racemase structural family by phylogenetic studies. Mol. Biol. Evol. 24, 79-89
2. Characterisation of a Pseudomonas aeruginosa twitching motility gene and evidence for a specialised protein export system widespread in eubacteria. Gene 101, 33-44
3. The sequence of a 22.4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine alpha-adaptin, as well as a new permease and a DNA-binding protein. Yeast 10, 1489-96
4. Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution. Biochemistry 36, 1329-42
5. Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases. Structure 7, 567-81