3ZK2
Crystal structure of the sodium binding rotor ring at pH 8.7
Summary for 3ZK2
| Entry DOI | 10.2210/pdb3zk2/pdb |
| Related | 3ZK1 |
| Descriptor | ATP SYNTHASE SUBUNIT C, SODIUM ION, DECYL-BETA-D-MALTOPYRANOSIDE, ... (4 entities in total) |
| Functional Keywords | membrane protein, hydrolase, rotor ring |
| Biological source | FUSOBACTERIUM NUCLEATUM |
| Total number of polymer chains | 22 |
| Total formula weight | 206710.23 |
| Authors | Schulz, S.,Meier, T.,Yildiz, O. (deposition date: 2013-01-21, release date: 2013-05-29, Last modification date: 2023-12-20) |
| Primary citation | Schulz, S.,Iglesias-Cans, M.,Krah, A.,Yildiz, O.,Leone, V.,Matthies, D.,Cook, G.M.,Faraldo-Gomez, J.D.,Meier, T. A new type of Na(+)-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif. PLoS Biol., 11:e1001596-e1001596, 2013 Cited by PubMed Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na⁺. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F₁F₀-ATP synthase with a novel Na⁺ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na⁺ specificity in physiological settings. Consistently, activity measurements showed Na⁺ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na⁺ ionophore monensin. Furthermore, Na⁺ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na⁺ coupling is provided by two identical crystal structures of the c₁₁ ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na⁺ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na⁺ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen. PubMed: 23824040DOI: 10.1371/journal.pbio.1001596 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.63 Å) |
Structure validation
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