7DO5
Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(apo-form)
Summary for 7DO5
| Entry DOI | 10.2210/pdb7do5/pdb |
| Descriptor | Short-chain dehydrogenase/reductase SDR, SULFATE ION (3 entities in total) |
| Functional Keywords | l-rhamnose metabolism, nadp-dependentdehydrogenase, sdr protein family, oxidoreductase |
| Biological source | Azotobacter vinelandii (strain DJ / ATCC BAA-1303) |
| Total number of polymer chains | 8 |
| Total formula weight | 224070.54 |
| Authors | Yoshiwara, K.,Watanabe, Y.,Watanabe, S. (deposition date: 2020-12-12, release date: 2021-02-03, Last modification date: 2023-11-29) |
| Primary citation | Yoshiwara, K.,Watanabe, S.,Watanabe, Y. Crystal structure of l-rhamnose 1-dehydrogenase involved in the nonphosphorylative pathway of l-rhamnose metabolism in bacteria. Febs Lett., 595:637-646, 2021 Cited by PubMed Abstract: Several microorganisms can utilize l-rhamnose as a carbon and energy source through the nonphosphorylative metabolic pathway, in which l-rhamnose 1-dehydrogenase (RhaDH) catalyzes the NAD(P) -dependent oxidization of l-rhamnose to l-rhamnono-1,4-lactone. We herein investigated the crystal structures of RhaDH from Azotobacter vinelandii in ligand-free, NAD -bound, NADP -bound, and l-rhamnose- and NAD -bound forms at 1.9, 2.1, 2.4, and 1.6 Å resolution, respectively. The significant interactions with the 2'-phosphate group of NADP , but not the 2'-hydroxyl group of NAD , were consistent with a preference for NADP over NAD . The C5-OH and C6-methyl groups of l-rhamnose were recognized by specific residues of RhaDH through hydrogen bonds and hydrophobic contact, respectively, which contribute to the different substrate specificities from other aldose 1-dehydrogenases in the short-chain dehydrogenase/reductase superfamily. PubMed: 33482017DOI: 10.1002/1873-3468.14046 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.836 Å) |
Structure validation
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