View source for 3wod


==RNA polymerase-gp39 complex==
<StructureSection load='3wod' size='340' side='right'caption='[[3wod]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3wod]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Thermus_virus_P23-45 Thermus virus P23-45]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WOD 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]] 3.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=3wod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wod OCA], [https://pdbe.org/3wod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wod RCSB], [https://www.ebi.ac.uk/pdbsum/3wod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wod ProSAT]</span></td></tr>
</table>
== Function ==
[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.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein encoded by Thermus thermophilus phage P23-45 binds the host's RNAP and inhibits transcription initiation from its major "-10/-35" class promoters. Phage promoters belonging to the minor "extended -10" class are minimally inhibited. We report the crystal structure of the T. thermophilus RNAP holoenzyme complexed with gp39, which explains the mechanism for RNAP promoter specificity switching. gp39 simultaneously binds to the RNAP beta-flap domain and the C-terminal domain of the sigma subunit (region 4 of the sigma subunit [sigma4]), thus relocating the beta-flap tip and sigma4. The ~45 A displacement of sigma4 is incompatible with its binding to the -35 promoter consensus element, thus accounting for the inhibition of transcription from -10/-35 class promoters. In contrast, this conformational change is compatible with the recognition of extended -10 class promoters. These results provide the structural bases for the conformational modulation of the host's RNAP promoter specificity to switch gene expression toward supporting phage development for gp39 and, potentially, other phage proteins, such as T4 AsiA.

Structural basis for promoter specificity switching of RNA polymerase by a phage factor.,Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S Genes Dev. 2014 Mar 1;28(5):521-31. doi: 10.1101/gad.233916.113. PMID:24589779<ref>PMID:24589779</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3wod" 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: Thermus thermophilus HB8]]
[[Category: Thermus virus P23-45]]
[[Category: Akasaka R]]
[[Category: Esyunina D]]
[[Category: Kulbachinskiy A]]
[[Category: Minakhin L]]
[[Category: Sekine S]]
[[Category: Severinov K]]
[[Category: Shirouzu M]]
[[Category: Tagami S]]
[[Category: Yokoyama S]]