1j7t: Difference between revisions
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==Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution== | ==Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution== | ||
<StructureSection load='1j7t' size='340' side='right' caption='[[1j7t]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='1j7t' size='340' side='right' caption='[[1j7t]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
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<table><tr><td colspan='2'>[[1j7t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7T FirstGlance]. <br> | <table><tr><td colspan='2'>[[1j7t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J7T FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7t OCA], [http://pdbe.org/1j7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7t RCSB], [http://www.ebi.ac.uk/pdbsum/1j7t PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j7t OCA], [http://pdbe.org/1j7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j7t RCSB], [http://www.ebi.ac.uk/pdbsum/1j7t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1j7t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
Revision as of 12:43, 4 October 2017
Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolutionComplex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution
Structural highlights
Publication Abstract from PubMedBACKGROUND: Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA. RESULTS: Crystals of complexes between oligoribonucleotides incorporating the sequence of the ribosomal A site of Escherichia coli and the aminoglycoside paromomycin have been solved at 2.5 A resolution. Each RNA fragment contains two A sites inserted between Watson-Crick pairs. The paromomycin molecules interact in an enlarged deep groove created by two bulging and one unpaired adenines. In both sites, hydroxyl and ammonium side chains of the antibiotic form 13 direct hydrogen bonds to bases and backbone atoms of the A site. In the best-defined site, 8 water molecules mediate 12 other hydrogen bonds between the RNA and the antibiotics. Ring I of paromomycin stacks over base G1491 and forms pseudo-Watson-Crick contacts with A1408. Both the hydroxyl group and one ammonium group of ring II form direct and water-mediated hydrogen bonds to the U1495oU1406 pair. The bulging conformation of the two adenines A1492 and A1493 is stabilized by hydrogen bonds between phosphate oxygens and atoms of rings I and II. The hydrophilic sites of the bulging A1492 and A1493 contact the shallow groove of G=C pairs in a symmetrical complex. CONCLUSIONS: Water molecules participate in the binding specificity by exploiting the antibiotic hydration shell and the typical RNA water hydration patterns. The observed contacts rationalize the protection, mutation, and resistance data. The crystal packing mimics the intermolecular contacts induced by aminoglycoside binding in the ribosome. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site.,Vicens Q, Westhof E Structure. 2001 Aug;9(8):647-58. PMID:11587639[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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