5WLY

E. coli LpxH- 8 mutations

5WLY の概要

• エントリーDOI: 10.2210/pdb5wly/pdb
• 分子名称: UDP-2,3-diacylglucosamine hydrolase, MANGANESE (II) ION, CHLORIDE ION, ... (6 entities in total)
• 機能のキーワード: lipid a synthesis, open conformation, udp-diacyl-glucosamine pyrophosphohydrolase, apha/beta-hydrolase, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27985.40

構造登録者

Bohl, T.E.,Aihara, H.,Shi, K.,Lee, J.K. (登録日: 2017-07-28, 公開日: 2018-04-11, 最終更新日: 2023-10-04)

主引用文献

Bohl, T.E.,Ieong, P.,Lee, J.K.,Lee, T.,Kankanala, J.,Shi, K.,Demir, O.,Kurahashi, K.,Amaro, R.E.,Wang, Z.,Aihara, H.
The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.
J. Biol. Chem., 293:7969-7981, 2018

PubMed Abstract: Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen-deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.

PubMed: 29626094
DOI: 10.1074/jbc.RA118.002503

実験手法

X-RAY DIFFRACTION (2 Å)