6WM6
Periplasmic EDTA-binding protein EppA, tetragonal
Summary for 6WM6
| Entry DOI | 10.2210/pdb6wm6/pdb |
| Descriptor | Extracellular solute-binding protein, family 5, SULFATE ION, 1,2-ETHANEDIOL, ... (4 entities in total) |
| Functional Keywords | periplasmic binding protein, edta, bioremediation, abc transporter, peptide binding protein |
| Biological source | Chelativorans sp. (strain BNC1) |
| Total number of polymer chains | 1 |
| Total formula weight | 63282.90 |
| Authors | Lewis, K.M.,Sattler, S.A.,Greene, C.L.,Xun, L.,Kang, C. (deposition date: 2020-04-20, release date: 2020-11-18, Last modification date: 2024-10-30) |
| Primary citation | Lewis, K.M.,Greene, C.L.,Sattler, S.A.,Youn, B.,Xun, L.,Kang, C. The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1. Int J Mol Sci, 21:-, 2020 Cited by PubMed Abstract: The widespread use of synthetic aminopolycarboxylates, such as ethylenediaminetetraacetate (EDTA), as chelating agents has led to their contamination in the environment as stable metal-chelate complexes. Microorganisms can transport free EDTA, but not metal-EDTA complexes, into cells for metabolism. An ABC-type transporter for free EDTA uptake in sp. BNC1 was investigated to understand the mechanism of the ligand selectivity. We solved the X-ray crystal structure of the periplasmic EDTA-binding protein (EppA) and analyzed its structure-function relations through isothermal titration calorimetry, site-directed mutagenesis, molecular docking, and quantum chemical analysis. EppA had high affinities for EDTA and other aminopolycarboxylates, which agrees with structural analysis, showing that its binding pocket could accommodate free aminopolycarboxylates. Further, key amino acid residues involved in the binding were identified. Our results suggest that EppA is a general binding protein for the uptake of free aminopolycarboxylates. This finding suggests that bacterial cells import free aminopolycarboxylates, explaining why stable metal-chelate complexes are resistant to degradation, as they are not transported into the cells for degradation. PubMed: 32486296DOI: 10.3390/ijms21113940 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.42 Å) |
Structure validation
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