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1i2x

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[[Image:1i2x.gif|left|200px]]
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{{STRUCTURE_1i2x| PDB=1i2x | SCENE= }}
{{STRUCTURE_1i2x| PDB=1i2x | SCENE= }}
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'''2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM'''
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===2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM===
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==Overview==
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The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Husken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup &amp; Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.
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(as it appears on PubMed at http://www.pubmed.gov), where 11333021 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11333021}}
==About this Structure==
==About this Structure==
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[[Category: A-type na]]
[[Category: A-type na]]
[[Category: Dna/rna hybrids']]
[[Category: Dna/rna hybrids']]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 19:30:25 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 10:19:56 2008''

Revision as of 07:19, 1 July 2008

Image:1i2x.png

Template:STRUCTURE 1i2x

2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM

Template:ABSTRACT PUBMED 11333021

About this Structure

Full crystallographic information is available from OCA.

Reference

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid., Tereshko V, Wallace ST, Usman N, Wincott FE, Egli M, RNA. 2001 Mar;7(3):405-20. PMID:11333021

Page seeded by OCA on Tue Jul 1 10:19:56 2008

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