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| | <StructureSection load='3n97' size='340' side='right'caption='[[3n97]], [[Resolution|resolution]] 3.25Å' scene=''> | | <StructureSection load='3n97' size='340' side='right'caption='[[3n97]], [[Resolution|resolution]] 3.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n97]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N97 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3N97 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n97]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N97 FirstGlance]. <br> |
| | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr> | | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3n4m|3n4m]], [[3k4g|3k4g]]</div></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=3n97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n97 OCA], [https://pdbe.org/3n97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n97 RCSB], [https://www.ebi.ac.uk/pdbsum/3n97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n97 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104]), b3295, JW3257, pez, phs, rpoA, sez ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3n97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n97 OCA], [http://pdbe.org/3n97 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n97 RCSB], [http://www.ebi.ac.uk/pdbsum/3n97 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n97 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715] [[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] | + | [[https://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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 25104]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: DNA-directed RNA polymerase]]
| + | |
| - | [[Category: Ecoli]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Birktoft, J J]] | + | [[Category: Thermus aquaticus]] |
| - | [[Category: Lara-Gonzalez, S]] | + | [[Category: Birktoft JJ]] |
| - | [[Category: Lawson, C L]] | + | [[Category: Lara-Gonzalez S]] |
| - | [[Category: Gene regulation-dna complex]]
| + | [[Category: Lawson CL]] |
| - | [[Category: Protein-dna interaction]] | + | |
| - | [[Category: Protein-protein interaction]]
| + | |
| - | [[Category: Transcription initiation]]
| + | |
| Structural highlights
Function
[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][1] [2]
Publication Abstract from PubMed
We demonstrate here that the alpha subunit C-terminal domain of Escherichia coli RNA polymerase (alphaCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of alphaCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A6-tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A6-tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A6-tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second alphaCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either alphaCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving alphaCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors.
The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element.,Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL Biochemistry. 2020 Dec 8;59(48):4523-4532. doi: 10.1021/acs.biochem.0c00571. Epub, 2020 Nov 18. PMID:33205945[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Minakhin L, Nechaev S, Campbell EA, Severinov K. Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol. 2001 Jan;183(1):71-6. PMID:11114902 doi:http://dx.doi.org/10.1128/JB.183.1.71-76.2001
- ↑ Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell. 2002 Mar;9(3):527-39. PMID:11931761
- ↑ Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL. The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry. 2020 Dec 8;59(48):4523-4532. doi: 10.1021/acs.biochem.0c00571. Epub, 2020 Nov 18. PMID:33205945 doi:http://dx.doi.org/10.1021/acs.biochem.0c00571
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