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| | ==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme== | | ==Crystal structure of the T. Thermophilus RNA polymerase holoenzyme== |
| - | <StructureSection load='2a6e' size='340' side='right' caption='[[2a6e]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='2a6e' size='340' side='right'caption='[[2a6e]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2a6e]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A6E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2a6e]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6E 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">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1iw7|1iw7]], [[1smy|1smy]], [[2a68|2a68]], [[2a69|2a69]], [[2a6h|2a6h]]</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=2a6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6e OCA], [https://pdbe.org/2a6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6e RCSB], [https://www.ebi.ac.uk/pdbsum/2a6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6e ProSAT], [https://www.topsan.org/Proteins/RSGI/2a6e TOPSAN]</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=2a6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6e OCA], [http://pdbe.org/2a6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a6e RCSB], [http://www.ebi.ac.uk/pdbsum/2a6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6e ProSAT], [http://www.topsan.org/Proteins/RSGI/2a6e TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPOZ_THET8 RPOZ_THET8]] 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/RPOA_THET8 RPOA_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_THET8 RPOC_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/Q5SKW1_THET8 Q5SKW1_THET8]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715] 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 (By similarity).[HAMAP-Rule:MF_00963] | + | [https://www.uniprot.org/uniprot/RPOA_THET8 RPOA_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| - | *[[Sigma factor|Sigma factor]] | + | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Large Structures]] |
| | [[Category: Thermus thermophilus]] | | [[Category: Thermus thermophilus]] |
| - | [[Category: Artsimovitch, I]] | + | [[Category: Artsimovitch I]] |
| - | [[Category: Igarashi, N]] | + | [[Category: Igarashi N]] |
| - | [[Category: Matsugaki, N]] | + | [[Category: Matsugaki N]] |
| - | [[Category: Perederina, A]] | + | [[Category: Perederina A]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Svetlov D]] |
| - | [[Category: Svetlov, D]] | + | [[Category: Svetlov V]] |
| - | [[Category: Svetlov, V]] | + | [[Category: Tahirov TH]] |
| - | [[Category: Tahirov, T H]] | + | [[Category: Vassylyev DG]] |
| - | [[Category: Vassylyev, D G]] | + | [[Category: Vassylyeva MN]] |
| - | [[Category: Vassylyeva, M N]] | + | [[Category: Wakatsuki S]] |
| - | [[Category: Wakatsuki, S]] | + | |
| - | [[Category: Bridge helix]]
| + | |
| - | [[Category: Rna polymerase holoenzyme]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Transcription regulation]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
RPOA_THET8 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.,Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG Cell. 2005 Aug 12;122(3):351-63. PMID:16096056[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell. 2005 Aug 12;122(3):351-63. PMID:16096056 doi:http://dx.doi.org/10.1016/j.cell.2005.07.014
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