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| ==Cryo-EM structure of a Q-engaged arrested complex== | | ==Cryo-EM structure of a Q-engaged arrested complex== |
| <StructureSection load='6jnx' size='340' side='right'caption='[[6jnx]], [[Resolution|resolution]] 4.08Å' scene=''> | | <SX load='6jnx' size='340' side='right' viewer='molstar' caption='[[6jnx]], [[Resolution|resolution]] 4.08Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[6jnx]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_sfi Bacteriophage sfi] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNX FirstGlance]. <br> | | <table><tr><td colspan='2'>[[6jnx]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_P21 Enterobacteria phage P21], [https://en.wikipedia.org/wiki/Enterobacteria_phage_SfI Enterobacteria phage SfI] and [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=6JNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JNX FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.08Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), Q ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1225789 Bacteriophage SfI])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></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=6jnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnx OCA], [https://pdbe.org/6jnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jnx RCSB], [https://www.ebi.ac.uk/pdbsum/6jnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnx ProSAT]</span></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6jnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnx OCA], [http://pdbe.org/6jnx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnx RCSB], [http://www.ebi.ac.uk/pdbsum/6jnx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnx ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://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] [[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium. | | [https://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Bacteriophage Q protein engages sigma-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for sigma-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (Q(I) and Q(II)) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, Q(I) forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well.
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| Structural basis of Q-dependent transcription antitermination.,Shi J, Gao X, Tian T, Yu Z, Gao B, Wen A, You L, Chang S, Zhang X, Zhang Y, Feng Y Nat Commun. 2019 Jul 2;10(1):2925. doi: 10.1038/s41467-019-10958-8. PMID:31266960<ref>PMID:31266960</ref>
| | ==See Also== |
| | | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| </div>
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| <div class="pdbe-citations 6jnx" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: Bacteriophage sfi]] | | [[Category: Enterobacteria phage P21]] |
| [[Category: DNA-directed RNA polymerase]] | | [[Category: Enterobacteria phage SfI]] |
| [[Category: Ecoli]] | | [[Category: Escherichia coli K-12]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Feng, Y]] | | [[Category: Feng Y]] |
| [[Category: Shi, J]] | | [[Category: Shi J]] |
| [[Category: Antitermination]]
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| [[Category: Dna]]
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| [[Category: Rna]]
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| [[Category: Rna polymerase]]
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| [[Category: Transcription]]
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