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| - | [[Image:2pwt.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group== |
| - | |PDB= 2pwt |SIZE=350|CAPTION= <scene name='initialview01'>2pwt</scene>, resolution 1.800Å
| + | <StructureSection load='2pwt' size='340' side='right'caption='[[2pwt]], [[Resolution|resolution]] 1.80Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=LHA:DOUBLY+FUNCTIONALIZED+PAROMOMYCIN+PM-II-162'>LHA</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[2pwt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PWT FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LHA:DOUBLY+FUNCTIONALIZED+PAROMOMYCIN+PM-II-162'>LHA</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pwt OCA], [https://pdbe.org/2pwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pwt RCSB], [https://www.ebi.ac.uk/pdbsum/2pwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pwt ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pwt OCA], [http://www.ebi.ac.uk/pdbsum/2pwt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pwt RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group'''
| + | [[Category: Francois B]] |
| - | | + | [[Category: Hanessian S]] |
| - | | + | [[Category: Kondo J]] |
| - | ==Overview==
| + | [[Category: Pachamuthu K]] |
| - | 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.
| + | [[Category: Szychowski J]] |
| - | | + | [[Category: Westhof E]] |
| - | ==About this Structure==
| + | |
| - | 2PWT is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PWT OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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., Kondo J, Pachamuthu K, Francois B, Szychowski J, Hanessian S, Westhof E, ChemMedChem. 2007 Nov 12;2(11):1631-1638. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17722211 17722211]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Francois, B.]] | + | |
| - | [[Category: Hanessian, S.]] | + | |
| - | [[Category: Kondo, J.]] | + | |
| - | [[Category: Pachamuthu, K.]] | + | |
| - | [[Category: Szychowski, J.]] | + | |
| - | [[Category: Westhof, E.]] | + | |
| - | [[Category: aminoglycoside]]
| + | |
| - | [[Category: haba group]]
| + | |
| - | [[Category: ribosomal decoding site]]
| + | |
| - | [[Category: rna]]
| + | |
| - | [[Category: x-ray analysis]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:41:48 2008''
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