{"doi":"10.1101/2022.04.19.488743","title":"Cryo-EM structures of Na <sup>+</sup> -pumping NADH-ubiquinone oxidoreductase from <i>Vibrio cholerae</i>","abstract":"SUMMARY The Na + -pumping NADH-ubiquinone oxidoreductase (Na + -NQR) couples electron transfer from NADH to ubiquinone with Na + -pumping, generating an electrochemical Na + gradient that is essential for energy-consuming reactions in bacteria. Since Na + -NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na + - NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-Å resolution. The structures reveal the arrangement of all six redox cofactors including riboflavin, whose position has been under debate, and a newly assigned 2Fe-2S NqrD/E cluster located between the membrane embedded NqrD and NqrE subunits. A large part of the hydrophilic NqrF near the cytoplasmic membrane surface is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe- 2S centers in NqrF and NqrD/E, consistent with physiologically relevant electron transfer. Two different types of specific inhibitors (korormicin A and aurachin D-42) bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The current inhibitor-bound structures reasonably explain our previous biochemical findings obtained by different chemistry-based experiments. This study provides a definite foundation for understanding the function of Na + -NQR and the molecular mechanism of its specific inhibitors to support molecular design of new antibiotics targeting the enzyme.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":306969,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.956,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":758229,"name":"Moe Ishikawa","orcid":"0000-0002-8620-1801","position":1,"is_corresponding":false},{"id":758230,"name":"Takahiro Masuya","orcid":"0000-0003-4950-0527","position":2,"is_corresponding":false},{"id":758232,"name":"Masatoshi Murai","orcid":"0000-0001-6601-2854","position":3,"is_corresponding":false},{"id":870948,"name":"Yuki Kitazumi","orcid":"0000-0001-6171-6457","position":4,"is_corresponding":false},{"id":318119,"name":"Nicole Butler","orcid":"0000-0002-8392-1328","position":5,"is_corresponding":false},{"id":870949,"name":"Takayuki Kato","orcid":"0000-0002-8879-6685","position":6,"is_corresponding":false},{"id":318121,"name":"Blanca Barquera","orcid":"0000-0003-0708-3438","position":7,"is_corresponding":false},{"id":373410,"name":"Hideto Miyoshi","orcid":"0000-0002-1792-554X","position":8,"is_corresponding":false},{"id":870947,"name":"Jun-ichi Kishikawa","orcid":"0000-0003-3913-7330","position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":null,"created_at":"2026-07-19T00:32:52.703737Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}