6ovr: Difference between revisions

<table><tr><td colspan='2'>[[6ovr]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis], [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] 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=6OVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OVR 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]] 2.843&#8491;</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=6ovr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ovr OCA], [https://pdbe.org/6ovr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ovr RCSB], [https://www.ebi.ac.uk/pdbsum/6ovr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ovr ProSAT]</span></td></tr>

[https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

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Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition sigma factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak-trigger-freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the sigma dissociation from the core enzyme.

 

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.,Shin Y, Hedglin M, Murakami KS Nucleic Acids Res. 2020 Jan 22. pii: 5713455. doi: 10.1093/nar/gkz1221. PMID:31965171<ref>PMID:31965171</ref>

 

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

 

*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]

*[[Sigma factor 3D structures|Sigma factor 3D structures]]

[[Category: Bacillus subtilis]]

[[Category: Thermus thermophilus]]

[[Category: Thermus thermophilus HB8]]

[[Category: Murakami KS]]

[[Category: Shin Y]]