2dd3
From Proteopedia
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[[Image:2dd3.gif|left|200px]] | [[Image:2dd3.gif|left|200px]] | ||
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| - | + | {{STRUCTURE_2dd3| PDB=2dd3 | SCENE= }} | |
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'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack''' | '''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 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] | ||
| - | [[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.]] | ||
| - | [[Category: | + | [[Category: Alternating sheared aa pair]] |
| - | [[Category: | + | [[Category: Kink-turn motif]] |
| - | [[Category: | + | [[Category: Rapid conformation exchange]] |
| - | [[Category: | + | [[Category: Rna secondary structure prediction]] |
| - | [[Category: | + | [[Category: Sequence specific a-minor motif]] |
| - | [[Category: | + | [[Category: Thermodynamic]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:11:59 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 21:12, 3 May 2008
An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/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 00:11:59 2008
