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Chapter 7 : Ribosomal Proteins and Their Structural Transitions on and off the Ribosome

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Abstract:

This chapter briefly reviews the structural data available, identifies similarities and differences, and illustrates some difficulties in using the structures of isolated components for insertion into the structures of whole ribosomes or subunits determined at lower resolution. An awareness of the possible differences in structure is necessary for an appreciation of the usefulness of structural studies of isolated components from a larger system such as the ribosome. The fraction of ribosomal proteins that has been structurally characterized is now more than one-third of all ribosomal proteins from bacteria. The chapter focuses on the domain arrangement of ribosomal proteins, and structural motifs. The extended conformations of some ribosomal proteins can be compared to proteins like calmodulin, which has a very elongated structure in one state while the α-helix that separates the two domains becomes bent in another state, with the effect that the protein adopts a more globular structure. L1 is a two-domain protein. The structure of L1 from shows the two domains in close contact. Domain II can be described as an insert in domain I. Thus, there are two connections between the domains. The structural investigations have clearly established that the ribosomal proteins are formed by stable domains with significant hydrophobic cores that would hardly alter their structures upon binding to the ribosome. Several ribosomal proteins are built of two or more domains, sometimes with significant flexibility between them. Long, more or less flexible loops also frequently occur in ribosomal proteins.

Citation: Al-Karadaghi S, Davydova N, Eliseikina I, Liljas A, Garber M, Nevskaya N, Nikonov S, Tishchenko S. 2000. Ribosomal Proteins and Their Structural Transitions on and off the Ribosome, p 63-72. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch7

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Figures

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1

Two conformations of ribosomal protein L1 from (left) and (right). The orientation of the lower domain (domain II) is identical in both models. The residues indicated in black are the totally conserved residues 132 to 135 (GPRG) in the lower domain and 217 to 219 (TMG) in the upper domain. These residues are thought to interact with the 23S rRNA. The rotation of the upper domain opens the space between the domains to allow for rRNA binding in the case of the structure.

Citation: Al-Karadaghi S, Davydova N, Eliseikina I, Liljas A, Garber M, Nevskaya N, Nikonov S, Tishchenko S. 2000. Ribosomal Proteins and Their Structural Transitions on and off the Ribosome, p 63-72. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch7
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References

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Tables

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Table 1

Relationships of eubacterial proteins and available structures

Citation: Al-Karadaghi S, Davydova N, Eliseikina I, Liljas A, Garber M, Nevskaya N, Nikonov S, Tishchenko S. 2000. Ribosomal Proteins and Their Structural Transitions on and off the Ribosome, p 63-72. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch7
Generic image for table
Table 2

Domain divisions of ribosome proteins as observed from structural analysis

Citation: Al-Karadaghi S, Davydova N, Eliseikina I, Liljas A, Garber M, Nevskaya N, Nikonov S, Tishchenko S. 2000. Ribosomal Proteins and Their Structural Transitions on and off the Ribosome, p 63-72. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch7
Generic image for table
Table 3

Structural classes of ribosomal proteins

Citation: Al-Karadaghi S, Davydova N, Eliseikina I, Liljas A, Garber M, Nevskaya N, Nikonov S, Tishchenko S. 2000. Ribosomal Proteins and Their Structural Transitions on and off the Ribosome, p 63-72. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch7

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