4ki2: Difference between revisions

Revision as of 08:53, 7 December 2022

Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA

Structural highlights

4ki2 is a 6 chain structure with sequence from Thermus aquaticus. This structure supersedes the now removed PDB entry 4gor. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	K
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]

Publication Abstract from PubMed

Structural studies of -10 promoter element recognition by domain 2 of the RNA polymerase sigma subunit [Feklistov & Darst (2011), Cell, 147, 1257-1269] reveal an unusual crystal-packing arrangement dominated by G-quartets. The 3'-terminal GGG motif of the oligonucleotide used in crystallization participates in G-quadruplex formation with GGG motifs from symmetry-related complexes. Stacking between neighboring G-quadruplexes results in the formation of pseudo-continuous four-stranded columns running throughout the length of the crystal (G-columns). Here, a new crystal form is presented with a different arrangement of G-columns and it is proposed that the fortuitous finding of G-quartet packing could be useful in engineering crystal contacts in protein-ssDNA complexes.

Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes.,Feklistov A, Darst SA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep;69(Pt 9):950-5. doi:, 10.1107/S1744309113020368. Epub 2013 Aug 19. PMID:23989139^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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:https://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
↑ Feklistov A, Darst SA. Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep;69(Pt 9):950-5. doi:, 10.1107/S1744309113020368. Epub 2013 Aug 19. PMID:23989139 doi:https://dx.doi.org/10.1107/S1744309113020368

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OCA

[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:https://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

[3] Feklistov A, Darst SA. Crystallographic analysis of an RNA polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA: quadruplex formation as a possible tool for engineering crystal contacts in protein-ssDNA complexes. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Sep;69(Pt 9):950-5. doi:, 10.1107/S1744309113020368. Epub 2013 Aug 19. PMID:23989139 doi:https://dx.doi.org/10.1107/S1744309113020368

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4ki2' size='340' side='right'caption='[[4ki2]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ki2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gor 4gor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KI2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KI2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ki2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4gor 4gor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KI2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KI2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
+</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 id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ugo|3ugo]], [[3ugp|3ugp]]</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=4ki2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ki2 OCA], [https://pdbe.org/4ki2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ki2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ki2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ki2 ProSAT]</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=4ki2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ki2 OCA], [http://pdbe.org/4ki2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ki2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ki2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ki2 ProSAT]</span></td></tr>
 </table>
 == 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]
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 25104]]
 [[Category: Large Structures]]
-[[Category: Darst, S A]]
+[[Category: Thermus aquaticus]]
-[[Category: Feklistov, A]]
+[[Category: Darst SA]]
-[[Category: G-quadruplex]]
+[[Category: Feklistov A]]
-[[Category: G-quartet]]
-[[Category: Promoter opening]]
-[[Category: Promoter recognition]]
-[[Category: Protein-dna binding]]
-[[Category: Ssdna]]
-[[Category: Ssdna-binding]]
-[[Category: Transcription initiation]]
-[[Category: Transcription-dna complex]]

4ki2: Difference between revisions

Revision as of 08:53, 7 December 2022

Crystallographic analysis of an RNA-polymerase sigma-subunit fragment complexed with -10 promoter element ssDNA

Structural highlights

Function

Publication Abstract from PubMed

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References

Contents

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