5uf3

<StructureSection load='5uf3' size='340' side='right' caption='[[5uf3]], [[NMR_Ensembles_of_Models | 8 NMR models]]' scene=''>

<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>

</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>

<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/>

[[Category: Chang, A T]]

[[Category: DeJong, E]]

[[Category: Nikonowicz, E P]]

[[Category: Tran, M]]

[[Category: Phage]]

[[Category: Rna]]

[[Category: Tetraloop]]