View source for 1ekd


==NMR AND MOLECULAR MODELING REVEAL THAT DIFFERENT HYDROGEN BONDING PATTERNS ARE POSSIBLE FOR GU PAIRS: ONE HYDROGEN BOND FOR EACH GU PAIR IN R(GGCGUGCC)2 AND TWO FOR EACH GU PAIR IN R(GAGUGCUC)2==
<StructureSection load='1ekd' size='340' side='right'caption='[[1ekd]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ekd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKD FirstGlance]. <br>
</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=1ekd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ekd OCA], [https://pdbe.org/1ekd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ekd RCSB], [https://www.ebi.ac.uk/pdbsum/1ekd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ekd ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
G.U pairs occur frequently and have many important biological functions. The stability of symmetric tandem G.U motifs depends both on the adjacent Watson-Crick base pairs, e.g., 5'G &gt; 5'C, and the sequence of the G.U pairs, i.e., 5'-UG-3' &gt; 5'-GU-3', where an underline represents a nucleotide in a G.U pair [Wu, M., McDowell, J. A., and Turner, D. H. (1995) Biochemistry 34, 3204-3211]. In particular, at 37 degrees C, the motif 5'-CGUG-3' is less stable by approximately 3 kcal/mol compared with other symmetric tandem G.U motifs with G-C as adjacent pairs: 5'-GGUC-3', 5'-GUGC-3', and 5'-CUGG-3'. The solution structures of r(GAGUGCUC)(2) and r(GGCGUGCC)(2) duplexes have been determined by NMR and restrained simulated annealing. The global geometry of both duplexes is close to A-form, with some distortions localized in the tandem G.U pair region. The striking discovery is that in r(GGCGUGCC)(2) each G.U pair apparently has only one hydrogen bond instead of the two expected for a canonical wobble pair. In the one-hydrogen-bond model, the distance between GO6 and UH3 is too far to form a hydrogen bond. In addition, the temperature dependence of the imino proton resonances is also consistent with the different number of hydrogen bonds in the G.U pair. To test the NMR models, U or G in various G.U pairs were individually replaced by N3-methyluridine or isoguanosine, respectively, thus eliminating the possibility of hydrogen bonding between GO6 and UH3. The results of thermal melting studies on duplexes with these substitutions support the NMR models.

Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).,Chen X, McDowell JA, Kierzek R, Krugh TR, Turner DH Biochemistry. 2000 Aug 1;39(30):8970-82. PMID:10913310<ref>PMID:10913310</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1ekd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Chen X]]
[[Category: Kierzek R]]
[[Category: Krugh TR]]
[[Category: McDowell JA]]
[[Category: Turner DH]]