4F8V

Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)

Summary for 4F8V

• Entry DOI: 10.2210/pdb4f8v/pdb
• Related: 4F8U
• Descriptor: RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'), (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside (3 entities in total)
• Functional Keywords: decording, ribosome, rna-antibiotic complex, rna/antibiotic
• Total number of polymer chains: 2
• Total formula weight: 14381.21

Authors

Kondo, J.,Koganei, M.,Kasahara, T. (deposition date: 2012-05-18, release date: 2012-08-15, Last modification date: 2024-03-20)

Primary citation

Kondo, J.,Koganei, M.,Kasahara, T.
Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.
Acs Med.Chem.Lett., 3:741-744, 2012

PubMed 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/π interactions, the unsaturated ring I of sisomicin with a partially planar conformation can share its π-electron density with G1491 and fits well within the A-site helix.

PubMed: 24900542
DOI: 10.1021/ml300145y

Experimental method

X-RAY DIFFRACTION (2.8 Å)