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| <SX load='6oul' size='340' side='right' viewer='molstar' caption='[[6oul]], [[Resolution|resolution]] 3.40Å' scene=''> | | <SX load='6oul' size='340' side='right' viewer='molstar' caption='[[6oul]], [[Resolution|resolution]] 3.40Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[6oul]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895], [http://en.wikipedia.org/wiki/Escherichia_coli_110957 Escherichia coli 110957] and [http://en.wikipedia.org/wiki/Escherichia_coli_2-427-07_s4_c3 Escherichia coli 2-427-07_s4_c3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OUL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OUL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6oul]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_110957 Escherichia coli 110957] 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=6OUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OUL FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <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]] 3.4Å</td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6n57|6n57]], [[6n58|6n58]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1444266 Escherichia coli 2-427-07_S4_C3]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1268975 Escherichia coli 110957]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oul OCA], [https://pdbe.org/6oul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oul RCSB], [https://www.ebi.ac.uk/pdbsum/6oul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oul 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=6oul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oul OCA], [http://pdbe.org/6oul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oul RCSB], [http://www.ebi.ac.uk/pdbsum/6oul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oul ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| == Function == | | == Function == |
- | [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] 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 (By similarity). [[http://www.uniprot.org/uniprot/A0A073G207_ECOLX A0A073G207_ECOLX]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/U9YPW3_ECOLX U9YPW3_ECOLX]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322][RuleBase:RU004279][SAAS:SAAS00054030] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/Q0P6L9_ECOLX Q0P6L9_ECOLX]] 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 primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963][SAAS:SAAS00535554] | + | [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;">
| + | |
- | == Publication Abstract from PubMed ==
| + | |
- | TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the betalobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on sigma(70) region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.
| + | |
| | | |
- | E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation.,Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA Elife. 2019 Dec 16;8. pii: 49375. doi: 10.7554/eLife.49375. PMID:31841111<ref>PMID:31841111</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 6oul" style="background-color:#fffaf0;"></div>
| + | |
- | == References ==
| + | |
- | <references/>
| + | |
| __TOC__ | | __TOC__ |
| </SX> | | </SX> |
- | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
- | [[Category: DNA-directed RNA polymerase]]
| + | |
| [[Category: Escherichia coli 110957]] | | [[Category: Escherichia coli 110957]] |
- | [[Category: Escherichia coli 2-427-07_s4_c3]] | + | [[Category: Escherichia coli K-12]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Campbell, E A]] | + | [[Category: Campbell EA]] |
- | [[Category: Chen, J]] | + | [[Category: Chen J]] |
- | [[Category: Chiu, C E]] | + | [[Category: Chiu CE]] |
- | [[Category: Darst, S A]] | + | [[Category: Darst SA]] |
- | [[Category: Dna promoter melting]]
| + | |
- | [[Category: Protein-dna complex]]
| + | |
- | [[Category: Rna polyermase]]
| + | |
- | [[Category: Transcription]]
| + | |
- | [[Category: Transcription initiation]]
| + | |