5wis

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'''Unreleased structure'''
 
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The entry 5wis is ON HOLD
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==Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P- and E-site tRNAs at 2.7A resolution==
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<StructureSection load='5wis' size='340' side='right'caption='[[5wis]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5wis]] is a 22 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WIS FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.703&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=MT9:(3R,4S,5S,7R,9E,11S,12R)-12-ETHYL-11-HYDROXY-3,5,7,11-TETRAMETHYL-2,8-DIOXOOXACYCLODODEC-9-EN-4-YL+3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSIDE'>MT9</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wis OCA], [https://pdbe.org/5wis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wis RCSB], [https://www.ebi.ac.uk/pdbsum/5wis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wis ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Antibiotics methymycin (MTM) and pikromycin (PKM), co-produced by Streptomyces venezuelae, represent minimalist macrolide protein synthesis inhibitors. Unlike other macrolides, which carry several side chains, a single desosamine sugar is attached to the macrolactone ring of MTM and PKM. In addition, the macrolactone scaffold of MTM is smaller than in other macrolides. The unusual structure of MTM and PKM and their simultaneous secretion by S. venezuelae bring about the possibility that two compounds would bind to distinct ribosomal sites. However, by combining genetic, biochemical and crystallographic studies, we demonstrate that MTM and PKM inhibit translation by binding to overlapping sites in the ribosomal exit tunnel. Strikingly, while MTM and PKM readily arrest the growth of bacteria, approximately 40% of cellular proteins continue to be synthesized even at saturating concentrations of the drugs. Gel electrophoretic analysis shows that compared to other ribosomal antibiotics, MTM and PKM prevent synthesis of a smaller number of cellular polypeptides illustrating a unique mode of action of these antibiotics.
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Authors: Almutairi, M.M., Svetlov, M.S., Hansen, D.A., Khabibullina, N.F., Klepacki, D., Kang, H.Y., Sherman, D.H., Vazquez-Laslop, N., Polikanov, Y.S., Mankin, A.S.
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Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins.,Almutairi MM, Svetlov MS, Hansen DA, Khabibullina NF, Klepacki D, Kang HY, Sherman DH, Vazquez-Laslop N, Polikanov YS, Mankin AS Nucleic Acids Res. 2017 Sep 19;45(16):9573-9582. doi: 10.1093/nar/gkx673. PMID:28934499<ref>PMID:28934499</ref>
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Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P-and E-site tRNAs at 2.7A resolution
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Polikanov, Y.S]]
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<div class="pdbe-citations 5wis" style="background-color:#fffaf0;"></div>
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[[Category: Sherman, D.H]]
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[[Category: Hansen, D.A]]
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==See Also==
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[[Category: Svetlov, M.S]]
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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[[Category: Almutairi, M.M]]
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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[[Category: Kang, H.Y]]
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== References ==
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[[Category: Klepacki, D]]
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<references/>
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[[Category: Mankin, A.S]]
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__TOC__
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[[Category: Khabibullina, N.F]]
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</StructureSection>
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[[Category: Vazquez-Laslop, N]]
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Almutairi MM]]
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[[Category: Hansen DA]]
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[[Category: Kang HY]]
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[[Category: Khabibullina NF]]
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[[Category: Klepacki D]]
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[[Category: Mankin AS]]
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[[Category: Polikanov YS]]
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[[Category: Sherman DH]]
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[[Category: Svetlov MS]]
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[[Category: Vazquez-Laslop N]]

Current revision

Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P- and E-site tRNAs at 2.7A resolution

PDB ID 5wis

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