2PWT
Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group
Summary for 2PWT
| Entry DOI | 10.2210/pdb2pwt/pdb |
| Descriptor | 22-mer of the ribosomal decoding site, DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 (3 entities in total) |
| Functional Keywords | aminoglycoside; haba group; ribosomal decoding site; x-ray analysis; rna, rna-antibiotic complex, rna/antibiotic |
| Total number of polymer chains | 2 |
| Total formula weight | 16078.00 |
| Authors | Kondo, J.,Pachamuthu, K.,Francois, B.,Szychowski, J.,Hanessian, S.,Westhof, E. (deposition date: 2007-05-13, release date: 2007-09-18, Last modification date: 2024-03-13) |
| Primary citation | Kondo, J.,Pachamuthu, K.,Francois, B.,Szychowski, J.,Hanessian, S.,Westhof, E. Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity Chemmedchem, 2:1631-1638, 2007 Cited by PubMed Abstract: The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2'' of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A-minor interaction between two bulged-out adenines from the A site and the codon-anticodon stem of the mRNA-tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the "on" state with two bulged out adenines, and 2) a new binding mode of 1 to an A-minor motif which stabilizes complex formation between the ribosome and the mRNA-tRNA complex regardless of whether the codon-anticodon stem is of the cognate or near-cognate type. PubMed: 17722211DOI: 10.1002/cmdc.200700113 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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