4P20

Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

Replaces:  2G5Q

Summary for 4P20

• Entry DOI: 10.2210/pdb4p20/pdb
• Descriptor: 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3', (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide (3 entities in total)
• Functional Keywords: aminoglycoside, haba group, ribosomal decoding site, x-ray analysis, rna, amikacin, rna-antibiotic complex, rna/antibiotic
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 15882.02

Authors

Kondo, J.,Francois, B.,Russell, R.J.M.,Murray, J.B.,Westhof, E. (deposition date: 2014-02-28, release date: 2014-05-07, Last modification date: 2023-12-27)

Primary citation

Kondo, J.,Francois, B.,Russell, R.J.,Murray, J.B.,Westhof, E.
Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.
Biochimie, 88:1027-1031, 2006

PubMed Abstract: Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site.

PubMed: 16806634
DOI: 10.1016/j.biochi.2006.05.017

Experimental method

X-RAY DIFFRACTION (2.7 Å)