View source for 7khb


==Escherichia coli RNA polymerase and rrnBP1 promoter open complex==
<StructureSection load='7khb' size='340' side='right'caption='[[7khb]], [[Resolution|resolution]] 3.53&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7khb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KHB 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]] 3.53&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</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=7khb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7khb OCA], [https://pdbe.org/7khb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7khb RCSB], [https://www.ebi.ac.uk/pdbsum/7khb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7khb 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 ==
Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) sigma(70) holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized alpha subunit carboxyl-terminal domains and scrunches the template DNA with the sigma finger and beta' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of sigma domain 2 that opens a gate for DNA loading and ejects sigma(1.1) from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to sigma(1.1) ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.

Structural basis of ribosomal RNA transcription regulation.,Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS Nat Commun. 2021 Jan 22;12(1):528. doi: 10.1038/s41467-020-20776-y. PMID:33483500<ref>PMID:33483500</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7khb" 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: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Murakami KS]]
[[Category: Qayyum MZ]]
[[Category: Shin Y]]