1i3y

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[[Image:1i3y.gif|left|200px]]
 
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==SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.==
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The line below this paragraph, containing "STRUCTURE_1i3y", creates the "Structure Box" on the page.
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<StructureSection load='1i3y' size='340' side='right'caption='[[1i3y]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1i3y]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I3Y FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene></td></tr>
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{{STRUCTURE_1i3y| PDB=1i3y | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1i3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3y OCA], [https://pdbe.org/1i3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i3y RCSB], [https://www.ebi.ac.uk/pdbsum/1i3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3y ProSAT]</span></td></tr>
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</table>
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'''SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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The A loop is an essential RNA component of the ribosome peptidyltransferase center that directly interacts with aminoacyl (A)-site tRNA. The A loop is highly conserved and contains a ubiquitous 2'-O-methyl ribose modification at position U2552. Here, we present the solution structure of a modified and unmodified A-loop RNA to define both the A-loop fold and the structural impact of the U2552 modification. Solution data reveal that the A-loop RNA has a compact structure that includes a noncanonical base pair between C2556 and U2552. NMR evidence is presented that the N3 position of C2556 has a shifted pKa and that protonation at C2556-N3 changes the C-U pair geometry. Our data indicate that U2552 methylation modifies the A-loop fold, in particular the dynamics and position of residues C2556 and U2555. We compare our structural data with the structure of the A loop observed in a recent 50S crystal structure [Ban, N., Nissen, P., Hansen, J., Moore, P. B. &amp; Steitz, T. A. (2000) Science 289, 905--920; Nissen, P., Hansen, J., Ban, N., Moore, P. B. &amp; Steitz, T. A. (2000) Science 289, 920--930]. The solution and crystal structures of the A loop are dramatically different, suggesting that a structural rearrangement of the A loop must occur on docking into the peptidyltransferase center. Possible roles of this docking event, the shifted pKa of C2556 and the U2552 2'-O-methylation in the mechanism of translation, are discussed.
The A loop is an essential RNA component of the ribosome peptidyltransferase center that directly interacts with aminoacyl (A)-site tRNA. The A loop is highly conserved and contains a ubiquitous 2'-O-methyl ribose modification at position U2552. Here, we present the solution structure of a modified and unmodified A-loop RNA to define both the A-loop fold and the structural impact of the U2552 modification. Solution data reveal that the A-loop RNA has a compact structure that includes a noncanonical base pair between C2556 and U2552. NMR evidence is presented that the N3 position of C2556 has a shifted pKa and that protonation at C2556-N3 changes the C-U pair geometry. Our data indicate that U2552 methylation modifies the A-loop fold, in particular the dynamics and position of residues C2556 and U2555. We compare our structural data with the structure of the A loop observed in a recent 50S crystal structure [Ban, N., Nissen, P., Hansen, J., Moore, P. B. &amp; Steitz, T. A. (2000) Science 289, 905--920; Nissen, P., Hansen, J., Ban, N., Moore, P. B. &amp; Steitz, T. A. (2000) Science 289, 920--930]. The solution and crystal structures of the A loop are dramatically different, suggesting that a structural rearrangement of the A loop must occur on docking into the peptidyltransferase center. Possible roles of this docking event, the shifted pKa of C2556 and the U2552 2'-O-methylation in the mechanism of translation, are discussed.
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==About this Structure==
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Solution structure of the A loop of 23S ribosomal RNA.,Blanchard SC, Puglisi JD Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3720-5. Epub 2001 Mar 20. PMID:11259644<ref>PMID:11259644</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3Y OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Solution structure of the A loop of 23S ribosomal RNA., Blanchard SC, Puglisi JD, Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3720-5. Epub 2001 Mar 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11259644 11259644]
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</div>
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[[Category: Blanchard, S C.]]
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<div class="pdbe-citations 1i3y" style="background-color:#fffaf0;"></div>
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[[Category: Puglisi, J D.]]
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== References ==
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[[Category: 23s rrna]]
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<references/>
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[[Category: A loop]]
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__TOC__
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[[Category: A site]]
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</StructureSection>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 19:32:42 2008''
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[[Category: Large Structures]]
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[[Category: Blanchard SC]]
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[[Category: Puglisi JD]]

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SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA.

PDB ID 1i3y

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