Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site.
The solution structure of kanamycin A interacting with a ribosomal A-site fragment was solved by transferred-NOE techniques and found to agree with the structure of the complex observed in the crystal. Despite the fast exchange conditions found for the interaction, the bound form was identified by NOESY spectroscopy. At 600 MHz, NOE effects are only observed for the RNA-associated antibiotic. Dissociation constants were measured by NMR spectroscopy for two sites of interaction (K(d1)=150+/-40 microM; K(d2)=360+/-50 microM). Furthermore, the effects of the Cu(II) ion on the antibiotic, on the RNA fragment that mimics the bacterial ribosomal A site, and on the complex formed between these two entities were analyzed. The study led to the proposal of a model that localizes the copper ion within the kanamycin-RNA complex.
Department of Chemistry, University of Siena, Via A. Moro, 53100 Siena, Italy.
Duccio
D
Balenci
Francesca
F
Bernardi
Luciano
L
Cellai
Nicola
N
D'Amelio
Elena
E
Gaggelli
Nicola
N
Gaggelli
Elena
E
Molteni
Gianni
G
Valensin
D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D000926:Anticodon / Q000235:genetics; D002413:Cations, Divalent / Q000737:chemistry / Q000494:pharmacology; D003062:Codon / Q000235:genetics; D003300:Copper / Q000737:chemistry / Q000494:pharmacology*; D007612:Kanamycin / Q000737:chemistry* / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics; D011485:Protein Binding / Q000187:drug effects; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism*
D000900:Anti-Bacterial Agents; D000926:Anticodon; D002413:Cations, Divalent; D003062:Codon; D009841:Oligonucleotides; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D007612:Kanamycin; D003300:Copper