6VPB
A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)
Summary for 6VPB
| Entry DOI | 10.2210/pdb6vpb/pdb |
| Descriptor | 6-phosphogluconate dehydrogenase, DI(HYDROXYETHYL)ETHER, ISOPROPYL ALCOHOL, ... (5 entities in total) |
| Functional Keywords | 6-phosphogluconate dehydrogenase, gluconacetobacter diazotrophicus, membrane-bound protein, 6-phospho-d-gluconate, nad+, oxidoreductase |
| Biological source | Gluconacetobacter diazotrophicus (strain ATCC 49037 / DSM 5601 / PAl5) |
| Total number of polymer chains | 2 |
| Total formula weight | 71970.01 |
| Authors | Rodriguez-Romero, A.,Rodriguez-Hernandez, A. (deposition date: 2020-02-02, release date: 2020-07-22, Last modification date: 2024-03-06) |
| Primary citation | Sarmiento-Pavia, P.D.,Rodriguez-Hernandez, A.,Rodriguez-Romero, A.,Sosa-Torres, M.E. The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs. Febs J., 288:1286-1304, 2021 Cited by PubMed Abstract: The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative pentose phosphate pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present in both the soluble and the membrane fractions of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA; e.g., Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD over NADP , delivering NADH to the membrane-bound NADH dehydrogenase of the microorganisms required by the terminal oxidases to reduce dioxygen to water for energy conservation. ENZYME: ECnonbreakingspace1.1.1.343. DATABASE: Structural data are available in PDB database under the accession number 6VPB. PubMed: 32621793DOI: 10.1111/febs.15472 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.87 Å) |
Structure validation
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