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| | <StructureSection load='6pmi' size='340' side='right'caption='[[6pmi]], [[Resolution|resolution]] 3.86Å' scene=''> | | <StructureSection load='6pmi' size='340' side='right'caption='[[6pmi]], [[Resolution|resolution]] 3.86Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pmi]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco45 Eco45], [http://en.wikipedia.org/wiki/Eco57 Eco57] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PMI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pmi]] 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], [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PMI FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.86Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoB, ECS88_4448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), rpoC, Z5561, ECs4911 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoZ, ECS88_4064 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), fliA, flaD, rpoF, b1922, JW1907 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6pmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmi OCA], [https://pdbe.org/6pmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pmi RCSB], [https://www.ebi.ac.uk/pdbsum/6pmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmi ProSAT]</span></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'>[http://proteopedia.org/fgij/fg.htm?mol=6pmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmi OCA], [http://pdbe.org/6pmi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pmi RCSB], [http://www.ebi.ac.uk/pdbsum/6pmi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmi ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPOC_ECO57 RPOC_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_ECO45 RPOB_ECO45]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO45 RPOZ_ECO45]] 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. [[http://www.uniprot.org/uniprot/FLIA_ECOLI FLIA_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes.[HAMAP-Rule:MF_00962]<ref>PMID:2644646</ref> <ref>PMID:3536871</ref> <ref>PMID:7590326</ref> <ref>PMID:8866483</ref> | + | [https://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] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | In bacteria, sigma(28) is the flagella-specific sigma factor that targets RNA polymerase (RNAP) to control the expression of flagella-related genes involving bacterial motility and chemotaxis. However, the structural mechanism of sigma(28) -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli sigma(28) -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how sigma(28) -RNAP recognizes promoter DNA through strong interactions with the -10 element, but weak contacts with the -35 element, to initiate transcription. In addition, we observed a distinct architecture in which the beta' zinc-binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between sigma4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by sigma(70) family factors to enhance transcription from promoters with weak sigma4/-35 element interactions.
| + | |
| | | | |
| - | Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.,Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956<ref>PMID:32484956</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>
| + | |
| - | <div class="pdbe-citations 6pmi" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Eco45]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Eco57]] | + | [[Category: Escherichia coli O157:H7]] |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli S88]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Liu, B]] | + | [[Category: Liu B]] |
| - | [[Category: Shi, W]] | + | [[Category: Shi W]] |
| - | [[Category: Rpof]]
| + | |
| - | [[Category: Sigma28]]
| + | |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription initiation complex]]
| + | |
| - | [[Category: Znr domain]]
| + | |
