2dd2

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[[Image:2dd2.gif|left|200px]]
[[Image:2dd2.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 2dd2 |SIZE=350|CAPTION= <scene name='initialview01'>2dd2</scene>
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The line below this paragraph, containing "STRUCTURE_2dd2", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=PR5:PURINE+RIBOSIDE-5&#39;-MONOPHOSPHATE'>PR5</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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|GENE=
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|DOMAIN=
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{{STRUCTURE_2dd2| PDB=2dd2 | SCENE= }}
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|RELATEDENTRY=[[2dd1|2DD1]], [[2dd3|2DD3]], [[1xv0|1XV0]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd2 OCA], [http://www.ebi.ac.uk/pdbsum/2dd2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dd2 RCSB]</span>
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}}
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'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack'''
'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack'''
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==About this Structure==
==About this Structure==
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2DD2 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD2 OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD2 OCA].
==Reference==
==Reference==
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16734425 16734425]
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16734425 16734425]
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[[Category: Protein complex]]
 
[[Category: Chen, G.]]
[[Category: Chen, G.]]
[[Category: Kennedy, S D.]]
[[Category: Kennedy, S D.]]
[[Category: Krugh, T R.]]
[[Category: Krugh, T R.]]
[[Category: Turner, D H.]]
[[Category: Turner, D H.]]
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[[Category: a-minor motif]]
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[[Category: A-minor motif]]
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[[Category: alternating]]
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[[Category: Alternating]]
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[[Category: conformation exchange]]
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[[Category: Conformation exchange]]
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[[Category: dynamic]]
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[[Category: Dynamic]]
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[[Category: kink-turn]]
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[[Category: Kink-turn]]
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[[Category: rna secondary structure]]
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[[Category: Rna secondary structure]]
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[[Category: sheared aa pair]]
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[[Category: Sheared aa pair]]
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[[Category: sheared ga pair]]
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[[Category: Sheared ga pair]]
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[[Category: thermodynamic]]
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[[Category: Thermodynamic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:11:47 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:33:03 2008''
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Revision as of 21:11, 3 May 2008

Image:2dd2.gif

Template:STRUCTURE 2dd2

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack


Overview

A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.

About this Structure

Full crystallographic information is available from OCA.

Reference

An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425 Page seeded by OCA on Sun May 4 00:11:47 2008

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