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| | ==T. thermophilus transcription initiation complex having a YYY discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 8 (RPo-CCC-8)== | | ==T. thermophilus transcription initiation complex having a YYY discriminator sequence and a nontemplate-strand length corresponding to TSS selection at position 8 (RPo-CCC-8)== |
| - | <StructureSection load='5e18' size='340' side='right' caption='[[5e18]], [[Resolution|resolution]] 3.30Å' scene=''> | + | <StructureSection load='5e18' size='340' side='right'caption='[[5e18]], [[Resolution|resolution]] 3.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5e18]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E18 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5e18]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E18 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]] 3.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5e17|5e17]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sigA, TTHA0532 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=5e18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e18 OCA], [https://pdbe.org/5e18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e18 RCSB], [https://www.ebi.ac.uk/pdbsum/5e18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e18 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5e18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e18 OCA], [http://pdbe.org/5e18 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e18 RCSB], [http://www.ebi.ac.uk/pdbsum/5e18 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e18 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/RPOA_THETH RPOA_THETH]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[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/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. |
| | <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 5e18" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5e18" 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: DNA-directed RNA polymerase]] | + | [[Category: Large Structures]] |
| | [[Category: Thermus thermophilus]] | | [[Category: Thermus thermophilus]] |
| - | [[Category: Thet8]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Ebright, R H]] | + | [[Category: Ebright RH]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Zhang Y]] |
| - | [[Category: Abortive]]
| + | |
| - | [[Category: Bacterial]]
| + | |
| - | [[Category: Consensus]]
| + | |
| - | [[Category: Discriminator]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Dna-directed rna polymerase]]
| + | |
| - | [[Category: Gene expression regulation]]
| + | |
| - | [[Category: Promoter region]]
| + | |
| - | [[Category: Protein conformation]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Scrunching]]
| + | |
| - | [[Category: Sigma]]
| + | |
| - | [[Category: Sigma factor]]
| + | |
| - | [[Category: Single-stranded]]
| + | |
| - | [[Category: Transcription initiation]]
| + | |
| - | [[Category: Transcription start site]]
| + | |
| - | [[Category: Transcription-dna-rna complex]]
| + | |
| Structural highlights
Function
RPOA_THET8 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
Publication Abstract from PubMed
In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.
Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.,Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881. PMID:26941320[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Winkelman JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE. Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection. Science. 2016 Mar 4;351(6277):1090-3. doi: 10.1126/science.aad6881. PMID:26941320 doi:http://dx.doi.org/10.1126/science.aad6881
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