Crystallographic Analysis of Drug and Inhibitor-Binding Structure of RND-Type Multidrug Exporter AcrB in Physiologically Relevant Asymmetric Crystals

  • Ryosuke Nakashima
  • Keisuke Sakurai
  • Akihito Yamaguchi
Part of the Methods in Molecular Biology book series (MIMB, volume 1700)


Xenobiotic extruding pumps have recently been known to be widely distributed in living organisms from mammalian to bacteria as a host-defense mechanism in cellular level. These pumps not only confer multidrug resistance of cancer cells and pathogenic bacteria but also cause hereditary diseases through the mutation. Our purposes are to elucidate the molecular structures and mechanisms of these xenobiotic exporters.

We had succeeded to determine the crystal structure of bacterial major multidrug exporter AcrB at 3.5 Å resolution (Murakami et al., Nature 419:587–593, 2002) and elucidated the structural bases of substrate recognition that the pump recognize the places and thus act as a “membrane vacuum cleaner.” After that we also determined the crystal structure of the drug-binding form of AcrB in space group C2 in which asymmetric unit contains structurally asymmetric homo-trimer of AcrB (Murakami et al., Nature 443:173–179, 2006; Nakashima et al., Nature 480:565–569, 2011; Nakashima et al., Nature 500:120–126, 2013). Analyses revealed the existence of a specific mechanism to recognize numerous substrates that the multisite binding is the base of multidrug recognition rather than induced-fit, and functional-rotation mechanism in which three monomers undergo a strictly coordinated sequential conformational change cycle of access, binding, and extrusion. Determination of physiological asymmetric AcrB structure was crucially important to understand these transport mechanisms.

Key words

Multidrug exporter AcrB RND family Crystallization X-ray Crystal structure Functional-rotation mechanism Peristaltic pump mechanism 



This work was supported by CREST, JST.


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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Ryosuke Nakashima
    • 1
  • Keisuke Sakurai
    • 1
  • Akihito Yamaguchi
    • 1
  1. 1.Department of Cell Membrane Biology, Institute of Scientific and Industrial ResearchOsaka UniversityIbarakiJapan

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