2dd2: Difference between revisions
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[[Image:2dd2.gif|left|200px]] | [[Image:2dd2.gif|left|200px]] | ||
'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack''' | {{Structure | ||
|PDB= 2dd2 |SIZE=350|CAPTION= <scene name='initialview01'>2dd2</scene> | |||
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|LIGAND= | |||
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'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: I. The major conformation with A6/A15/A16 stack''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2DD2 is a [ | 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]. | ||
==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:// | 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: Protein complex]] | ||
[[Category: Chen, G.]] | [[Category: Chen, G.]] | ||
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[[Category: alternating]] | [[Category: alternating]] | ||
[[Category: conformation exchange]] | [[Category: conformation exchange]] | ||
[[Category: | [[Category: dynamic]] | ||
[[Category: kink-turn]] | [[Category: kink-turn]] | ||
[[Category: rna secondary structure]] | [[Category: rna secondary structure]] | ||
[[Category: sheared aa pair]] | [[Category: sheared aa pair]] | ||
[[Category: sheared ga pair]] | [[Category: sheared ga pair]] | ||
[[Category: | [[Category: thermodynamic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:25:48 2008'' | ||
Revision as of 14:25, 20 March 2008
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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
2DD2 is a Protein complex structure of sequences from [1]. 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
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