5B19
Picrophilus torridus aspartate racemase
Summary for 5B19
| Entry DOI | 10.2210/pdb5b19/pdb |
| Descriptor | Aspartate racemase, L(+)-TARTARIC ACID (3 entities in total) |
| Functional Keywords | aspartate racemase, picrophilus torridus, archaea, d-amino acid, isomerase |
| Biological source | Picrophilus torridus (strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828) |
| Total number of polymer chains | 2 |
| Total formula weight | 52068.03 |
| Authors | Aihara, T.,Ito, T.,Yamanaka, Y.,Noguchi, K.,Odaka, M.,Sekine, M.,Homma, H.,Yohda, M. (deposition date: 2015-11-30, release date: 2016-06-22, Last modification date: 2023-11-08) |
| Primary citation | Aihara, T.,Ito, T.,Yamanaka, Y.,Noguchi, K.,Odaka, M.,Sekine, M.,Homma, H.,Yohda, M. Structural and functional characterization of aspartate racemase from the acidothermophilic archaeon Picrophilus torridus Extremophiles, 20:385-393, 2016 Cited by PubMed Abstract: Functional and structural characterizations of pyridoxal 5'-phosphate-independent aspartate racemase of the acidothermophilic archaeon Picrophilus torridus were performed. Picrophilus aspartate racemase exhibited high substrate specificity to aspartic acid. The optimal reaction temperature was 60 °C, which is almost the same as the optimal growth temperature. Reflecting the low pH in the cytosol, the optimal reaction pH of Picrophilus aspartate racemase was approximately 5.5. However, the activity at the putative cytosolic pH of 4.6 was approximately 6 times lower than that at the optimal pH of 5.5. The crystal structure of Picrophilus aspartate racemase was almost the same as that of other pyridoxal 5'-phosphate -independent aspartate racemases. In two molecules of the dimer, one molecule contained a tartaric acid molecule in the catalytic site; the structure of the other molecule was relatively flexible. Finally, we examined the intracellular existence of D-amino acids. Unexpectedly, the proportion of D-aspartate to total aspartate was not very high. In contrast, both D-proline and D-alanine were observed. Because Picrophilus aspartate racemase is highly specific to aspartate, other amino acid racemases might exist in Picrophilus torridus. PubMed: 27094682DOI: 10.1007/s00792-016-0829-7 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.851 Å) |
Structure validation
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