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Open Access Research article

A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis

Qinglan Guo1, Jingwei Weng2, Xiaogang Xu1, Minghua Wang1, Xiaoying Wang1, Xinyu Ye1, Wenning Wang23* and Minggui Wang13*

Author Affiliations

1 Institute of Antibiotics, Huashan Hospital Fudan University, 12 Wulumuqi Road, Shanghai 200040, China

2 Department of Chemistry, Fudan University,220 Handan Road, Shanghai 200433, China

3 Institute of Biomedical Sciences, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China

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BMC Structural Biology 2010, 10:33  doi:10.1186/1472-6807-10-33

Published: 8 October 2010

Abstract

Background

The first report on the transferable, plasmid-mediated quinolone-resistance determinant qnrA1 was in 1998. Since then, qnr alleles have been discovered worldwide in clinical strains of Gram-negative bacilli. Qnr proteins confer quinolone resistance, and belong to the pentapeptide repeat protein (PRP) family. Several PRP crystal structures have been solved, but little is known about the functional significance of their structural arrangement.

Results

We conducted random and site-directed mutagenesis on qnrA1 and on qnrC, a newly identified quinolone-resistance gene from Proteus mirabilis. Many of the Qnr mutants lost their quinolone resistance function. The highly conserved hydrophobic Leu or Phe residues at the center of the pentapeptide repeats are known as i sites, and loss-of-function mutations included replacement of the i site hydrophobic residues with charged residues, replacing the i-2 site, N-terminal to the i residues, with bulky side-chain residues, introducing Pro into the β-helix coil, deletion of the N- and C-termini, and excision of a central coil. Molecular dynamics simulations and homology modeling demonstrated that QnrC overall adopts a stable β-helix fold and shares more similarities with MfpA than with other PRP structures. Based on homology modeling and molecular dynamics simulation, the dysfunctional point mutations introduced structural deformations into the quadrilateral β-helix structure of PRPs. Of the pentapeptides of QnrC, two-thirds adopted a type II β-turn, while the rest adopted type IV turns. A gap exists between coil 2 and coil 3 in the QnrC model structure, introducing a structural flexibility that is similar to that seen in MfpA.

Conclusion

The hydrophobic core and the β-helix backbone conformation are important for maintaining the quinolone resistance property of Qnr proteins. QnrC may share structural similarity with MfpA.