10.5452/MA-D04S6
Ramaswamy, Venkata Krishnan; Vargiu, Attilio Vittorio; Malloci, Giuliano; Dreier, Jürg; Ruggerone, Paolo
Multidrug transporter MexY of Pseudomonas aeruginosa
modelarchive.org
2019
3D macromolecular model
2019-01-07
en
Secondary multidrug transporters of the resistance-nodulation-cell division (RND) superfamily contribute crucially to antibiotic resistance in Gram-negative bacteria. Compared to the most studied transporter AcrB of E. coli, little is known about the molecular determinants of distinct polyspecificities of the most important RND transporters MexB and MexY of Pseudomonas aeruginosa. The absence of an experimental structure of MexY and the availability of only one structure of MexB bound to compounds (the ABI-PP inhibitor D13-9001) have made it hard to reach this goal. However, given the overall good sequence identity and similarity of MexY with MexB of P. aeruginosa and with AcrB of E. coli for which high-resolution X-ray structures are available, reliable computational modelling of MexY and related structure-based studies are possible. Here, we present a thoroughly validated MexY structure generated by template-based homology modelling using the high-resolution crystal structures of AcrB (PDB ID: 4DX5, 1.9 Å) and MexB (PDB ID: 3W9I, 2.7 Å) as the templates. The model was built using Modeller 9.13 and subjected to various geometric and stereochemical quality factors to evaluate backbone angles, side chain flips, rotamers, steric clashes etc. using state-of-the-art bioinformatics tools. The stability of the MexY model, as well as its suitability for subsequent analyses, were validated in four independent μs-long MD simulations. This work represents the first comparative study of the major RND transporters in P. aeruginosa and also the first structure-based study of MexY, for which no experimental structure is available yet.