2dd3: Difference between revisions

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[[Image:2dd3.gif|left|200px]]
{{Seed}}
[[Image:2dd3.png|left|200px]]


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{{STRUCTURE_2dd3|  PDB=2dd3  |  SCENE=  }}  
{{STRUCTURE_2dd3|  PDB=2dd3  |  SCENE=  }}  


'''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===




==Overview==
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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.
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{{ABSTRACT_PUBMED_16734425}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA].  
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA].  


==Reference==
==Reference==
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[[Category: Sequence specific a-minor motif]]
[[Category: Sequence specific a-minor motif]]
[[Category: Thermodynamic]]
[[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 Tue Jul 29 03:13:42 2008''

Revision as of 00:13, 29 July 2008

File:2dd3.png

Template:STRUCTURE 2dd3

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack

Template:ABSTRACT PUBMED 16734425

About this Structure

Full experimental 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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