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Chapter 38 : Structure and Function of the Sarcin-Ricin Domain

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Structure and Function of the Sarcin-Ricin Domain, Page 1 of 2

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Abstract:

The sarcin-ricin domain (SRD) of 23S rRNA, which includes a near-universal, purine rich sequence of 12 nucleotides, is the site of action of the eponymous ribotoxins. The chapter focuses on the structure of SRD. There is an evidence that the SRD constitutes an important part of the elongation factor G (EF-G) binding site. The three SRD purines that are protected from chemical modification by EF-G bound to ribosomes are presumptive EF-G identity elements. A number of mutations have been made in the SRD in an 23S rRNA gene. The mutations have been constructed in a plasmid carrying an operon. This operon has a transcription unit with the genes for 16S, 23S, and 5S rRNAs. There is biochemical and genetic evidence that the flexible region in the SRD affects the binding of the elongation factors. There are differences in the structures of the flexible regions of the rat and SRDs. There are three nucleotides in the SRD that are protected from chemical modification by both EF-G and the EF-Tu ternary complex. The EF-Tu ternary complex may bind to the ribosome only when peptidyl-tRNA is in the P site (posttranslocation), and EF-G may bind only when it is in the A site.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38

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Figures

Image of Figure 1
Figure 1

Structure of the SRD. (a) Ribbon diagram with separate modules color coded. (b) Base-stacking diagram; to delineate the cross-strand stacks, the nucleotides on the 5′ side are in solid boxes and those on the 3′ side are in open boxes.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 2
Figure 2

SRD GAGA tetraloop and its closing C•G pair.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 3
Figure 3

(a) SRD G-bulged cross-strand A stack. (b) Diagram of the A stack; the arrows indicate the chain direction. The significance of the open and closed boxes and of the colors is given in the legend to Fig. 1.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 4
Figure 4

SRD flexible region. The refined model superimposed on the 2 - electron density map showing how the water-mediated base pairs stitch the flexible region nucleotides together. The asterisks designate water molecules that form ideal bridging contacts.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 5
Figure 5

The SRD S-turn. The reversal of chain direction is indicated by arrows; C2′- sugar puckers are designated by asterisks.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 6
Figure 6

Comparison of the structures of the and rat SRDs. Shown are ribbon diagrams with the helical stems superimposed.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 7
Figure 7

Binding of EF-G to SRD oligoribonucleotides. (A) Gel retardation assay. (B) The results in A plotted to show that binding saturates and that when the reactants are equimolar (10 μM) the complex has 70% of the input RNA.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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Image of Figure 8
Figure 8

The two faces of the SRD. On the left is an orthogonal view of the solvent-accessible surface of the domain—the surface to which the elongation factors and toxins presumably bind. On the right, the buried surface is designated by yellow ellipses.

Citation: Wool I, Correll C, Chan Y. 2000. Structure and Function of the Sarcin-Ricin Domain, p 461-474. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch38
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