|
|
| Line 3: |
Line 3: |
| | <SX load='6n58' size='340' side='right' viewer='molstar' caption='[[6n58]], [[Resolution|resolution]] 3.78Å' scene=''> | | <SX load='6n58' size='340' side='right' viewer='molstar' caption='[[6n58]], [[Resolution|resolution]] 3.78Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6n58]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N58 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N58 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6n58]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N58 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]] 3.78Å</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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6n58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n58 OCA], [http://pdbe.org/6n58 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n58 RCSB], [http://www.ebi.ac.uk/pdbsum/6n58 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n58 ProSAT]</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=6n58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n58 OCA], [https://pdbe.org/6n58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n58 RCSB], [https://www.ebi.ac.uk/pdbsum/6n58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n58 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/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/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/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/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] |
| - | <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 6n58" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Escherichia coli]] |
| | [[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]]
| + | |
| - | [[Category: Transferase]]
| + | |
