Determination of Pentapeptide Repeat Units in Qnr Proteins by the Structure-Based Alignment Approach

The Qnr proteins belong to the pentapeptide repeat protein family. Despite each pentapeptide repeat unit being an important structural determinant, accurately determining pentapeptide repeat units in the Qnr proteins through sequence-based alignments has been challenging. In the present study, the pentapeptide repeat units of the nine representative Qnr proteins have been precisely determined via the structure-based alignment approach using homology modeling and superposition of their best models. The plasmid-mediated quinolone resistance gene, qnr (later renamed qnrA1), was first described from a ciprofloxacin-resistant strain of Klebsiella pneumoniae in 1998 (13, 21). Many additional qnr genes, such as qnrS1, qnrB1, qnrC, and qnrD, have since been discovered from plasmids or the bacterial chromosome (5, 7, 9, 10, 25). With the recently discovered qnrAS (20), qnrSM (19), qnrVP (15), and qnrVV (15), the Qnr proteins currently comprise nine families, QnrA, QnrS, QnrB, QnrC, QnrD, QnrAS, QnrSM, QnrVP, and QnrVV, which differ from each other in amino acid sequence by 30 % or more