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| | ==Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA== | | ==Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA== |
| - | <StructureSection load='4xlr' size='340' side='right' caption='[[4xlr]], [[Resolution|resolution]] 4.30Å' scene=''> | + | <StructureSection load='4xlr' size='340' side='right'caption='[[4xlr]], [[Resolution|resolution]] 4.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xlr]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104], [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_jl-18 Thermus thermophilus jl-18]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XLR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XLR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xlr]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus], [https://en.wikipedia.org/wiki/Thermus_thermophilus_JL-18 Thermus thermophilus JL-18] 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=4XLR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XLR 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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xln|4xln]], [[4xlp|4xlp]], [[4xlq|4xlq]], [[4xls|4xls]], [[4xax|4xax]]</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=4xlr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xlr OCA], [https://pdbe.org/4xlr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xlr RCSB], [https://www.ebi.ac.uk/pdbsum/4xlr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xlr ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sigA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104]), TtJL18_0238 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=798128 Thermus thermophilus JL-18])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xlr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xlr OCA], [http://pdbe.org/4xlr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xlr RCSB], [http://www.ebi.ac.uk/pdbsum/4xlr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xlr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] 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.<ref>PMID:11158566</ref> [[http://www.uniprot.org/uniprot/SIGA_THEAQ SIGA_THEAQ]] 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]<ref>PMID:11114902</ref> <ref>PMID:11931761</ref> | + | [https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4xlr" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4xlr" 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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 25104]] | + | [[Category: Large Structures]] |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Synthetic construct]] |
| | [[Category: Thermus aquaticus]] | | [[Category: Thermus aquaticus]] |
| - | [[Category: Thermus thermophilus jl-18]] | + | [[Category: Thermus thermophilus JL-18]] |
| - | [[Category: Bae, B]] | + | [[Category: Bae B]] |
| - | [[Category: Darst, S A]] | + | [[Category: Darst SA]] |
| - | [[Category: Bacterial transcription initiation complex]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Transcription-dna complex]]
| + | |
| Structural highlights
Function
RPOA_THEAQ
Publication Abstract from PubMed
A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.
CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.,Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08505. PMID:26349034[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA. CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08505. PMID:26349034 doi:http://dx.doi.org/10.7554/eLife.08505
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