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Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.

ABSTRACT: Sisomicin with an unsaturated sugar ring I displays better antibacterial activity than other structurally related aminoglycosides, such as gentamicin, tobramycin, and amikacin. In the present study, we have confirmed by X-ray analyses that the binding mode of sisomicin is basically similar but not identical to that of the related compounds having saturated ring I. A remarkable difference is found in the stacking interaction between ring I and G1491. While the typical saturated ring I with a chair conformation stacks on G1491 through CH/? interactions, the unsaturated ring I of sisomicin with a partially planar conformation can share its ?-electron density with G1491 and fits well within the A-site helix.

SUBMITTER: Kondo J

PROVIDER: S-EPMC4025859 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

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Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.

Kondo Jiro J Koganei Mai M Kasahara Tomoko T

ACS medicinal chemistry letters 20120802 9

Sisomicin with an unsaturated sugar ring I displays better antibacterial activity than other structurally related aminoglycosides, such as gentamicin, tobramycin, and amikacin. In the present study, we have confirmed by X-ray analyses that the binding mode of sisomicin is basically similar but not identical to that of the related compounds having saturated ring I. A remarkable difference is found in the stacking interaction between ring I and G1491. While the typical saturated ring I with a chai ...[more]

PMID: 24900542

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