6cae: Difference between revisions

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-'''Unreleased structure'''
-The entry 6cae is ON HOLD
+==Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution==
+<StructureSection load='6cae' size='340' side='right'caption='[[6cae]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6cae]] is a 20 chain structure with sequence from [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=6CAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CAE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<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=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=EUP:(2~{S},3~{S})-2,4-bis(azanyl)-3-oxidanyl-butanoic+acid'>EUP</scene>, <scene name='pdbligand=IAR:(2E)-5-[(DIAMINOMETHYLIDENE)AMINO]-2-IMINOPENTANOIC+ACID'>IAR</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=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=ORD:D-ORNITHINE'>ORD</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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6cae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cae OCA], [https://pdbe.org/6cae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cae RCSB], [https://www.ebi.ac.uk/pdbsum/6cae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cae ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL14_THET8 RL14_THET8] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367]  Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Growing resistance of pathogenic bacteria and shortage of antibiotic discovery platforms challenge the use of antibiotics in the clinic. This threat calls for exploration of unconventional sources of antibiotics and identification of inhibitors able to eradicate resistant bacteria. Here we describe a different class of antibiotics, odilorhabdins (ODLs), produced by the enzymes of the non-ribosomal peptide synthetase gene cluster of the nematode-symbiotic bacterium Xenorhabdus nematophila. ODLs show activity against Gram-positive and Gram-negative pathogens, including carbapenem-resistant Enterobacteriaceae, and can eradicate infections in animal models. We demonstrate that the bactericidal ODLs interfere with protein synthesis. Genetic and structural analyses reveal that ODLs bind to the small ribosomal subunit at a site not exploited by current antibiotics. ODLs induce miscoding and promote hungry codon readthrough, amino acid misincorporation, and premature stop codon bypass. We propose that ODLs' miscoding activity reflects their ability to increase the affinity of non-cognate aminoacyl-tRNAs to the ribosome.
-Authors: Pantel, L., Florin, T., Dobosz-Bartoszek, M., Racine, E., Sarciaux, M., Serri, M., Houard, J., Campagne, J.M., Marcia de Figueiredo, R., Midrier, C., Gaudriault, S., Givaudan, A., Lanois, A., Forst, S., Aumelas, A., Cotteaux-Lautard, C., Bolla, J.M., Vingsbo Lundberg, C., Huseby, D., Hughes, D., Villain-Guillot, P., Mankin, A.S., Polikanov, Y.S., Gualtieri, M.
+Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site.,Pantel L, Florin T, Dobosz-Bartoszek M, Racine E, Sarciaux M, Serri M, Houard J, Campagne JM, de Figueiredo RM, Midrier C, Gaudriault S, Givaudan A, Lanois A, Forst S, Aumelas A, Cotteaux-Lautard C, Bolla JM, Vingsbo Lundberg C, Huseby DL, Hughes D, Villain-Guillot P, Mankin AS, Polikanov YS, Gualtieri M Mol Cell. 2018 Apr 5;70(1):83-94.e7. doi: 10.1016/j.molcel.2018.03.001. PMID:29625040<ref>PMID:29625040</ref>
-Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P-and E-site tRNAs at 2.6A resolution
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Serri, M]]
+<div class="pdbe-citations 6cae" style="background-color:#fffaf0;"></div>
-[[Category: Polikanov, Y.S]]
-[[Category: Florin, T]]
+==See Also==
-[[Category: Bolla, J.M]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-[[Category: Pantel, L]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-[[Category: Houard, J]]
+== References ==
-[[Category: Lanois, A]]
+<references/>
-[[Category: Forst, S]]
+__TOC__
-[[Category: Sarciaux, M]]
+</StructureSection>
-[[Category: Mankin, A.S]]
+[[Category: Large Structures]]
-[[Category: Hughes, D]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Gualtieri, M]]
+[[Category: Aumelas A]]
-[[Category: Cotteaux-Lautard, C]]
+[[Category: Bolla JM]]
-[[Category: Villain-Guillot, P]]
+[[Category: Campagne JM]]
-[[Category: Marcia De Figueiredo, R]]
+[[Category: Cotteaux-Lautard C]]
-[[Category: Huseby, D]]
+[[Category: Dobosz-Bartoszek M]]
-[[Category: Campagne, J.M]]
+[[Category: Florin T]]
-[[Category: Dobosz-Bartoszek, M]]
+[[Category: Forst S]]
-[[Category: Midrier, C]]
+[[Category: Gaudriault S]]
-[[Category: Gaudriault, S]]
+[[Category: Givaudan A]]
-[[Category: Givaudan, A]]
+[[Category: Gualtieri M]]
-[[Category: Vingsbo Lundberg, C]]
+[[Category: Houard J]]
-[[Category: Aumelas, A]]
+[[Category: Hughes D]]
-[[Category: Racine, E]]
+[[Category: Huseby D]]
+[[Category: Lanois A]]
+[[Category: Mankin AS]]
+[[Category: Marcia de Figueiredo R]]
+[[Category: Midrier C]]
+[[Category: Pantel L]]
+[[Category: Polikanov YS]]
+[[Category: Racine E]]
+[[Category: Sarciaux M]]
+[[Category: Serri M]]
+[[Category: Villain-Guillot P]]
+[[Category: Vingsbo Lundberg C]]