6JNJ
Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)
Summary for 6JNJ
| Entry DOI | 10.2210/pdb6jnj/pdb |
| Descriptor | L-arabinose 1-dehydrogenase (NAD(P)(+)), PHOSPHATE ION (3 entities in total) |
| Functional Keywords | l-arabinose metabolism, nadp-dependent dehydrogenase, gfo/idh/moca protein family, oxidoreductase |
| Biological source | Azospirillum brasilense |
| Total number of polymer chains | 2 |
| Total formula weight | 68175.29 |
| Authors | Watanabe, Y.,Iga, C.,Watanabe, S. (deposition date: 2019-03-16, release date: 2019-05-15, Last modification date: 2023-11-22) |
| Primary citation | Watanabe, Y.,Iga, C.,Watanabe, Y.,Watanabe, S. Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase. Febs Lett., 593:1257-1266, 2019 Cited by PubMed Abstract: In Azospirillum brasilense, a gram-negative nitrogen-fixing bacterium, l-arabinose is converted to α-ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway, l-arabinose is oxidized to l-arabino-γ-lactone by NAD(P)-dependent l-arabinose 1-dehydrogenase (AraDH) belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo- and NADP-bound AraDH at 1.5 and 2.2 Å resolutions, respectively. A docking model of l-arabinose and NADP-bound AraDH and structure-based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination between l-arabinose and d-xylose, the C4 epimer of l-arabinose. PubMed: 31058311DOI: 10.1002/1873-3468.13424 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.5 Å) |
Structure validation
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