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==Crystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolution== | |||
<StructureSection load='7jql' size='340' side='right'caption='[[7jql]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7jql]] 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=7JQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JQL 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]] 3Å</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=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=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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7jql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jql OCA], [https://pdbe.org/7jql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jql RCSB], [https://www.ebi.ac.uk/pdbsum/7jql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jql ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Proline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens. | |||
Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens.,Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borisek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M J Med Chem. 2020 Aug 13. doi: 10.1021/acs.jmedchem.0c00665. PMID:32787108<ref>PMID:32787108</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7jql" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Beckert | ==See Also== | ||
[[Category: | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: Di Stasi | __TOC__ | ||
[[Category: Hilpert | </StructureSection> | ||
[[Category: Mardirossian | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus thermophilus HB8]] | ||
[[Category: | [[Category: Armas F]] | ||
[[Category: | [[Category: Beckert B]] | ||
[[Category: | [[Category: Borisek J]] | ||
[[Category: | [[Category: Buchmann J]] | ||
[[Category: | [[Category: Collis DWP]] | ||
[[Category: Di Stasi A]] | |||
[[Category: Hilpert K]] | |||
[[Category: Magistrato A]] | |||
[[Category: Mardirossian M]] | |||
[[Category: Polikanov YS]] | |||
[[Category: Scocchi M]] | |||
[[Category: Sola R]] | |||
[[Category: Syroegin EA]] | |||
[[Category: Valencic E]] | |||
[[Category: Wilson DN]] | |||
Latest revision as of 09:33, 12 February 2025
Crystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolutionCrystal structure of the Thermus thermophilus 70S ribosome in complex with Bac7-001, mRNA, and deacylated P-site tRNA at 3.00A resolution
Structural highlights
Publication Abstract from PubMedProline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens. Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens.,Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borisek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M J Med Chem. 2020 Aug 13. doi: 10.1021/acs.jmedchem.0c00665. PMID:32787108[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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