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==Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)==
==Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)==
<StructureSection load='3ugp' size='340' side='right' caption='[[3ugp]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='3ugp' size='340' side='right'caption='[[3ugp]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ugp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UGP FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ugp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UGP FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.697&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ugo|3ugo]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ugp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ugp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ugp RCSB], [http://www.ebi.ac.uk/pdbsum/3ugp PDBsum]</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=3ugp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ugp OCA], [https://pdbe.org/3ugp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ugp RCSB], [https://www.ebi.ac.uk/pdbsum/3ugp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ugp ProSAT]</span></td></tr>
<table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[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>  
The key step in bacterial promoter opening is recognition of the -10 promoter element (T(-12)A(-11)T(-10)A(-9)A(-8)T(-7) consensus sequence) by the RNA polymerase sigma subunit. We determined crystal structures of sigma domain 2 bound to single-stranded DNA bearing-10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every -10 element nucleotide. Base-specific interactions occur primarily with A(-11) and T(-7), which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the -10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by sigma. These results provide a detailed structural basis for the critical roles of A(-11) and T(-7) in promoter melting and reveal important insights into the initiation of transcription bubble formation.
 
Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit.,Feklistov A, Darst SA Cell. 2011 Dec 9;147(6):1257-69. Epub 2011 Dec 1. PMID:22136875<ref>PMID:22136875</ref>


From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
[[Category: Darst, S A.]]
[[Category: Darst SA]]
[[Category: Feklistov, A.]]
[[Category: Feklistov A]]
[[Category: Bacterial promoter opening]]
[[Category: Dna binding]]
[[Category: G-quadruplex]]
[[Category: G-quartet]]
[[Category: Protein-dna complex]]
[[Category: Transcription-dna complex]]

Latest revision as of 16:57, 14 March 2024

Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)Crystal structure of RNA-polymerase sigma subunit domain 2 complexed with -10 promoter element ssDNA oligo (TATAAT)

Structural highlights

3ugp is a 3 chain structure with sequence from Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.697Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

See Also

References

  1. ↑ 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
  2. ↑ 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

3ugp, resolution 2.70Å

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