6kqh: Difference between revisions
No edit summary |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 7 nt== | |||
<StructureSection load='6kqh' size='340' side='right'caption='[[6kqh]], [[Resolution|resolution]] 3.18Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6kqh]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] 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=6KQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KQH 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]] 3.18Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6kqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kqh OCA], [https://pdbe.org/6kqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kqh RCSB], [https://www.ebi.ac.uk/pdbsum/6kqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kqh 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 == | |||
All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "sigma-finger" of the bacterial transcription initiation factor sigma. The structures reveal that-for both the primary sigma-factor and extracytoplasmic (ECF) sigma-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "sigma-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from approximately 5 nt to approximately 10 nt. | |||
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.,Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y Proc Natl Acad Sci U S A. 2020 Mar 3. pii: 1920747117. doi:, 10.1073/pnas.1920747117. PMID:32127479<ref>PMID:32127479</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6kqh" 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: Synthetic construct]] | |||
[[Category: Thermus thermophilus HB8]] | |||
[[Category: Ebright RH]] | |||
[[Category: Li L]] | |||
[[Category: Zhang Y]] | |||
Latest revision as of 13:39, 22 November 2023
Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 7 ntThermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 7 nt
Structural highlights
FunctionRPOA_THET8 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Publication Abstract from PubMedAll organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "sigma-finger" of the bacterial transcription initiation factor sigma. The structures reveal that-for both the primary sigma-factor and extracytoplasmic (ECF) sigma-factors, and for both 5'-triphosphate RNA and 5'-hydroxy RNA-the "sigma-finger" is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5'-end, upon extension of nascent RNA from approximately 5 nt to approximately 10 nt. RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.,Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y Proc Natl Acad Sci U S A. 2020 Mar 3. pii: 1920747117. doi:, 10.1073/pnas.1920747117. PMID:32127479[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||