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==E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)== | |||
<StructureSection load='6uu4' size='340' side='right'caption='[[6uu4]], [[Resolution|resolution]] 4.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6uu4]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] 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=6UU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UU4 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]] 4.305Å</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=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=6uu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu4 OCA], [https://pdbe.org/6uu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uu4 RCSB], [https://www.ebi.ac.uk/pdbsum/6uu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RPOS_ECOLI RPOS_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959]<ref>PMID:15558318</ref> <ref>PMID:15716429</ref> <ref>PMID:16511888</ref> <ref>PMID:21398637</ref> <ref>PMID:8475100</ref> Protects stationary phase cells from killing induced by endoribonuclease MazF.<ref>PMID:19251848</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
In bacteria, the dissociable sigma subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the sigma factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the sigma(3.2) loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the sigma(3) domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and sigma-RNAP core separation to transition transcription from initiation to elongation. | |||
Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.,Zuo Y, De S, Feng Y, Steitz TA iScience. 2020 Aug 11;23(9):101445. doi: 10.1016/j.isci.2020.101445. PMID:32829286<ref>PMID:32829286</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6uu4" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: De | ==See Also== | ||
*[[Sigma factor 3D structures|Sigma factor 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Escherichia coli]] | |||
[[Category: Escherichia coli K-12]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: De S]] | |||
[[Category: Steitz TA]] | |||
[[Category: Zuo Y]] | |||
Latest revision as of 10:58, 11 October 2023
E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)
Structural highlights
FunctionRPOS_ECOLI Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959][1] [2] [3] [4] [5] Protects stationary phase cells from killing induced by endoribonuclease MazF.[6] Publication Abstract from PubMedIn bacteria, the dissociable sigma subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the sigma factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the sigma(3.2) loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the sigma(3) domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and sigma-RNAP core separation to transition transcription from initiation to elongation. Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.,Zuo Y, De S, Feng Y, Steitz TA iScience. 2020 Aug 11;23(9):101445. doi: 10.1016/j.isci.2020.101445. PMID:32829286[7] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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