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==Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator==
==Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator==
<StructureSection load='5uf3' size='340' side='right' caption='[[5uf3]], [[NMR_Ensembles_of_Models | 8 NMR models]]' scene=''>
<StructureSection load='5uf3' size='340' side='right'caption='[[5uf3]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5uf3]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UF3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5uf3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_GA Enterobacteria phage GA]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UF3 FirstGlance]. <br>
</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=5uf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf3 OCA], [http://pdbe.org/5uf3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf3 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf3 ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=5uf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf3 OCA], [https://pdbe.org/5uf3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uf3 RCSB], [https://www.ebi.ac.uk/pdbsum/5uf3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf3 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of a RNA hairpin containing the RNA operator binding site for bacteriophage GA coat protein is presented. The phage GA operator contains the asymmetric (A-A)-U sequence motif and is capped by a four-adenine (tetra-A) loop. The uridine of the (A-A)-U motif preferentially pairs with the 5'-proximal cross-strand adenine, and the 3'-proximal adenine stacks into the helix. The tetra-A loop is well-ordered with adenine residues 2-4 forming a 3' stack. This loop conformation stands in contrast to the structure of the 5'-AUUA loop of the related phage MS2 operator in which residues 1 and 2 form a 5' stack. The context dependence of the (A-A)-U sequence motif conformation was examined using structures of 76 unique occurrences from the Protein Data Bank. The motif almost always has one adenine bulged and the other adenine adopting an A-U base pair. In the case in which the (A-A)-U motif is flanked by only one Watson-Crick base pair, the adenine adjacent to the flanking base pair tends to bulge; 80% of motifs with a 3' flanking pair have a 3' bulged adenine, and 84% of motifs with a 5' flanking pair have a 5' bulged adenine. The frequencies of 3'- and 5'-proximal adenines bulging are 33 and 67%, respectively, when the (A-A)-U motif is flanked by base pairs on both sides. Although a 3' flanking cytidine correlates (88%) with bulging of the 5'-proximal adenine, no strict dependence on flanking nucleotide identity was identified for the 5' side.
Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator.,Chang AT, Tran M, Nikonowicz EP Biochemistry. 2017 May 30;56(21):2690-2700. doi: 10.1021/acs.biochem.7b00123., Epub 2017 May 17. PMID:28488852<ref>PMID:28488852</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5uf3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chang, A T]]
[[Category: Enterobacteria phage GA]]
[[Category: DeJong, E]]
[[Category: Large Structures]]
[[Category: Nikonowicz, E P]]
[[Category: Chang AT]]
[[Category: Tran, M]]
[[Category: DeJong E]]
[[Category: Phage]]
[[Category: Nikonowicz EP]]
[[Category: Rna]]
[[Category: Tran M]]
[[Category: Rna hairpin]]
[[Category: Tetraloop]]

Latest revision as of 07:28, 1 May 2024

Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator

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