9ynq: Difference between revisions
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==Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)== | |||
<StructureSection load='9ynq' size='340' side='right'caption='[[9ynq]], [[Resolution|resolution]] 3.32Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9ynq]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9YNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9YNQ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.32Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1CYH:(2~{S})-~{N}-[[(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-2-(2-carbamimidamidoethanoylamino)pentanediamide'>A1CYH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=9ynq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ynq OCA], [https://pdbe.org/9ynq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ynq RCSB], [https://www.ebi.ac.uk/pdbsum/9ynq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ynq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Pseudouridimycin (PUM) is a C-nucleoside/peptide antibiotic that selectively inhibits bacterial RNA polymerase (RNAP) and exhibits potent activity against drug-resistant pathogens. However, PUM suffers from chemical instability due to self-immolative cleavage of its central hydroxamate bond. Here, we employed cryo-electron microscopy to determine structures of PUM (1) and a chemically stabilized des-hydroxy analog of PUM (2a) bound to an Escherichia coli RNAP transcription complex. Guided by the observed bound conformation, we developed an efficient solid-phase synthesis of 50 des-hydroxy PUM analogs modified at the Gln residue and Gdn-Gly tail. Several analogs retained low-micromolar RNAP-inhibitory activity, with a para-substituted phenyl amidine analog (54) emerging as the most potent inhibitor (IC(50) = 0.95 muM). These results establish a versatile synthetic platform and structural framework for optimizing stabilized PUM derivatives and provide a foundation for the development of RNAP-targeted therapeutics against resistant bacterial pathogens. | |||
Solid-phase synthesis and biological evaluation of des-hydroxy pseudouridimycin analogs.,Anwar AF, You L, Degen D, Burns KJ, Garza MJ, Ebright RH, Del Valle JR ACS Med Chem Lett. 2026 Mar 11:10.1021/acsmedchemlett.5c00684. doi: , 10.1021/acsmedchemlett.5c00684. PMID:41890570<ref>PMID:41890570</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9ynq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli str. K-12 substr. MG1655]] | |||
[[Category: Large Structures]] | |||
[[Category: Ebright RH]] | |||
[[Category: You LL]] | |||
Revision as of 06:36, 8 April 2026
Cryo-EM structure of Escherichia coli transcription initiation complex with GpA and des-hydroxy pseudouridimycin (des-hydroxy PUM)
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