4wap | pdb_00004wap

Crystal structure of the E. coli ribosome bound to negamycin. This file contains the 50S subunit of the first 70S ribosome.

spinqualitylabelsall models 4wap, resolution 3.09Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4wap is a 31 chain structure with sequence from Escherichia coli, Escherichia coli str. k-12 substr. mg1655 and Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG, ZN Related: 4wao, 4waq, 4war Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 A resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation. Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.,Olivier NB, Altman RB, Noeske J, Basarab GS, Code E, Ferguson AD, Gao N, Huang J, Juette MF, Livchak S, Miller MD, Prince DB, Cate JH, Buurman ET, Blanchard SC Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201414401. PMID:25368144 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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