5EN5

Apo structure of bacterial efflux pump.

5EN5 の概要

• エントリーDOI: 10.2210/pdb5en5/pdb
• 分子名称: Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB, DARPin (3 entities in total)
• 機能のキーワード: efflux pump, transport protein
• 由来する生物種: Escherichia coli (strain K12); 詳細
• 細胞内の位置: Cell inner membrane ; Multi- pass membrane protein : P31224
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 252174.67

構造登録者

Sjuts, H.,Ornik, A.R.,Pos, K.M. (登録日: 2015-11-09, 公開日: 2016-04-06, 最終更新日: 2024-01-10)

主引用文献

Sjuts, H.,Vargiu, A.V.,Kwasny, S.M.,Nguyen, S.T.,Kim, H.S.,Ding, X.,Ornik, A.R.,Ruggerone, P.,Bowlin, T.L.,Nikaido, H.,Pos, K.M.,Opperman, T.J.
Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives.
Proc.Natl.Acad.Sci.USA, 113:3509-3514, 2016

PubMed Abstract: The Escherichia coli AcrAB-TolC efflux pump is the archetype of the resistance nodulation cell division (RND) exporters from Gram-negative bacteria. Overexpression of RND-type efflux pumps is a major factor in multidrug resistance (MDR), which makes these pumps important antibacterial drug discovery targets. We have recently developed novel pyranopyridine-based inhibitors of AcrB, which are orders of magnitude more powerful than the previously known inhibitors. However, further development of such inhibitors has been hindered by the lack of structural information for rational drug design. Although only the soluble, periplasmic part of AcrB binds and exports the ligands, the presence of the membrane-embedded domain in AcrB and its polyspecific binding behavior have made cocrystallization with drugs challenging. To overcome this obstacle, we have engineered and produced a soluble version of AcrB [AcrB periplasmic domain (AcrBper)], which is highly congruent in structure with the periplasmic part of the full-length protein, and is capable of binding substrates and potent inhibitors. Here, we describe the molecular basis for pyranopyridine-based inhibition of AcrB using a combination of cellular, X-ray crystallographic, and molecular dynamics (MD) simulations studies. The pyranopyridines bind within a phenylalanine-rich cage that branches from the deep binding pocket of AcrB, where they form extensive hydrophobic interactions. Moreover, the increasing potency of improved inhibitors correlates with the formation of a delicate protein- and water-mediated hydrogen bond network. These detailed insights provide a molecular platform for the development of novel combinational therapies using efflux pump inhibitors for combating multidrug resistant Gram-negative pathogens.

PubMed: 26976576
DOI: 10.1073/pnas.1602472113

実験手法

X-RAY DIFFRACTION (2.3 Å)