9LRR

Cryo-EM structure of Na+-translocating NADH-ubiquinone oxidoreductase NqrB-G141A mutant from Vibrio cholerae with bound korormicin A

Summary for 9LRR

• Entry DOI: 10.2210/pdb9lrr/pdb
• EMDB information: 63340
• Descriptor: Na(+)-translocating NADH-quinone reductase subunit A, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, Korormicin, ... (15 entities in total)
• Functional Keywords: na+-nqr, na+ transporter, inhibitor, oxidoreductase, drug resistant, membrane protein
• Biological source: Vibrio cholerae O395; More
• Total number of polymer chains: 6
• Total formula weight: 217424.37

Authors

Ishikawa-Fukuda, M.,Kishikawa, J.,Kato, T.,Murai, M. (deposition date: 2025-02-01, release date: 2025-04-23, Last modification date: 2025-05-21)

Primary citation

Ishikawa-Fukuda, M.,Kishikawa, J.I.,Masuya, T.,Ito, T.,Butler, N.L.,McFee, D.,Kato, T.,Barquera, B.,Miyoshi, H.,Murai, M.
Structural Elucidation of the Mechanism for Inhibitor Resistance in the Na + -Translocating NADH-Ubiquinone Oxidoreductase from Vibrio cholerae.
Biochemistry, 64:1963-1972, 2025

PubMed Abstract: Na-translocating NADH-ubiquinone oxidoreductase (Na-NQR) is a unique redox-driven Na-pump. Since this enzyme is exclusively found in prokaryotes, including the human pathogens and , it is a promising target for highly selective antibiotics. Korormicin A, a natural product, and a specific and potent inhibitor of Na-NQR, may become a lead compound for the relevant drug design. We previously showed that the G141A mutation in the NqrB subunit (NqrB-G141A) confers moderate resistance to korormicin A (about 100-fold). However, the efficiency of photoaffinity labeling of the mutant enzyme by a photoreactive korormicin derivative was the same as in the wild-type enzyme. Because of these apparently conflicting results, the molecular mechanism underlying the korormicin A-resistance remains elusive. In the present study, we determined the cryo-EM structure of the NqrB-G141A mutant in the presence of bound korormicin A, and compared it to the corresponding structure from the wild-type enzyme. The toxophoric moiety of korormicin A binds to the mutant enzyme similarly to how it binds to the wild type. However, the added bulk of the alanine-141 excludes the alkyl side chain from the binding cavity, resulting in a decrease in the binding affinity. In fact, isothermal titration calorimetry revealed that the binding affinity of korormicin to the NqrB-G141A mutant is significantly weaker compared to the wild-type. Altogether, we conclude that the inhibitory potency of korormicin A is weaker in the NqrB-G141A mutant due to the decrease in its binding affinity to the altered binding cavity.

PubMed: 40263754
DOI: 10.1021/acs.biochem.5c00069

Experimental method

ELECTRON MICROSCOPY (2.68 Å)