1i3x: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
New page: left|200px<br /><applet load="1i3x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1i3x" /> '''SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBO...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1i3x.gif|left|200px]]<br /><applet load="1i3x" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1i3x" />
'''SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA'''<br />


==Overview==
==SOLUTION STRUCTURE OF THE A LOOP OF 23S RIBOSOMAL RNA==
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.
<StructureSection load='1i3x' size='340' side='right'caption='[[1i3x]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1i3x]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I3X 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=1i3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3x OCA], [https://pdbe.org/1i3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i3x RCSB], [https://www.ebi.ac.uk/pdbsum/1i3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3x ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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>
1I3X is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1I3X OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11259644 11259644]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1i3x" style="background-color:#fffaf0;"></div>
[[Category: Blanchard, S.C.]]
== References ==
[[Category: Puglisi, J.D.]]
<references/>
[[Category: 23s rrna]]
__TOC__
[[Category: a loop]]
</StructureSection>
[[Category: a site]]
[[Category: Large Structures]]
 
[[Category: Blanchard SC]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:33:40 2007''
[[Category: Puglisi JD]]
Retrieved from "https://proteopedia.org/1i3x"