View source for 6vvv


==Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase==
<StructureSection load='6vvv' size='340' side='right'caption='[[6vvv]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6vvv]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VVV 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]] 3.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6vvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vvv OCA], [https://pdbe.org/6vvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vvv RCSB], [https://www.ebi.ac.uk/pdbsum/6vvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vvv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RBPA_MYCS2 RBPA_MYCS2] Binds to RNA polymerase (RNAP), probably stimulating transcriptions from principal, but not alternative sigma factor promoters (By similarity). Partially restores transcription in the presence of rifampicin (Rif) in vitro; overexpression leads to an increase in the Rif tolerance in vivo, with smaller colonies. Seems to act by removing Rif from its binding site and preventing its further binding. No longer stimulates transcription in Rif-resistant RNA polymerase (with mutations in rpoB).<ref>PMID:19926651</ref> <ref>PMID:21415119</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Rifampicin (Rif) is a first-line therapeutic used to treat the infectious disease tuberculosis (TB), which is caused by the pathogen Mycobacterium tuberculosis (Mtb). The emergence of Rif-resistant (Rif(R)) Mtb presents a need for new antibiotics. Rif targets the enzyme RNA polymerase (RNAP). Sorangicin A (Sor) is an unrelated inhibitor that binds in the Rif-binding pocket of RNAP. Sor inhibits a subset of Rif(R) RNAPs, including the most prevalent clinical Rif(R) RNAP substitution found in Mtb infected patients (S456&gt;L of the beta subunit). Here, we present structural and biochemical data demonstrating that Sor inhibits the wild-type Mtb RNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the Rif(R) S456L enzyme at an earlier step, preventing the transition of a partially unwound promoter DNA intermediate to the fully opened DNA and blocking the template-strand DNA from reaching the active site in the RNAP catalytic center. By defining template-strand blocking as a mechanism for inhibition, we provide a mechanistic drug target in RNAP. Our finding that Sor inhibits the wild-type and mutant RNAPs through different mechanisms prompts future considerations for designing antibiotics against resistant targets. Also, we show that Sor has a better pharmacokinetic profile than Rif, making it a suitable starting molecule to design drugs to be used for the treatment of TB patients with comorbidities who require multiple medications.

The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.,Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Muller R, Mooney R, Landick R, Darst SA, Campbell EA Proc Natl Acad Sci U S A. 2020 Nov 16. pii: 2013706117. doi:, 10.1073/pnas.2013706117. PMID:33199626<ref>PMID:33199626</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6vvv" style="background-color:#fffaf0;"></div>

==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycolicibacterium smegmatis MC2 155]]
[[Category: Synthetic construct]]
[[Category: Campbell EA]]
[[Category: Darst SA]]
[[Category: Lilic M]]