1i2x

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spinqualitylabelsall models 1i2x, resolution 2.4Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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

Overview

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 & 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.

About this Structure

1I2X is a Protein complex structure of sequences from [1] with SPD as ligand. 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

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