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Chapter 9 : Structure and Evolution of the 23S rRNA Binding Domain of Protein L2

Authors: Isao Tanaka1, Atsushi Nakagawa1, Takashi Nakashima1, Masae Taniguchi1, Harumi Hosaka1, Makoto Kimura2
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Affiliations: 1: Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan; 2: Laboratory of Biochemistry, Faculty of Agriculture, Kyushu University, Fukuoka 812-8512, Japan
Content Type: Monograph
Publication Year: 2000

Category: Microbial Genetics and Molecular Biology

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Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, Page 1 of 2

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Abstract:

This chapter focuses on the crystal structure of the RNA binding domain of L2, and discusses its structure from functional and evolutionary points of view. Site-directed mutagenesis of Arg86 or Arg155 significantly diminished RNA binding affinity, and in addition, Arg68 and Lys70 mutations caused partial loss of RNA binding. To date, the three-dimensional structures of over a dozen ribosomal proteins have been determined. Comparison of their structures with those of other known proteins in the Protein Data Bank revealed that many ribosomal proteins share structural motifs, such as RNP, dsRNA binding domain, KH domain, and helix-turn-helix motifs, with RNA or DNA binding proteins. Recent studies of ribosomes, however, demonstrated that peptidyltransferase activity is never attributed solely to the 23S rRNA, and they reduce the number of possible essential macromolecular components of the peptidyltransferase center to 23S rRNA and ribosomal proteins L2 and L3.

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9

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Structure and Evolution of the 23S rRNA Binding Domain of Protein L2
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Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
/content/10.1128/9781555818142.chap9.fig9-1
Figure 1

Stereo view of L2-RBD. The molecule consists of two subdomains of approximately equal size. The N-terminal domain has an OB fold homologous to the S1 domain, and the C-terminal domain has an SH3-like-barrel motif. The fifth -strand and a 3 helix (H1) connect two subdomains.

10.1128/9781555818142/fig9-1_thmb.gif
10.1128/9781555818142/fig9-1.gif
Image of Figure 1
Figure 1

Stereo view of L2-RBD. The molecule consists of two subdomains of approximately equal size. The N-terminal domain has an OB fold homologous to the S1 domain, and the C-terminal domain has an SH3-like-barrel motif. The fifth -strand and a 3 helix (H1) connect two subdomains.

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
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Figure 2

Topological diagram showing secondary structure of L2-RBD. The molecule consists of 10 -strands (indicated by arrows) and a short 3 helix (indicated by a rectangle). Unlike in the ordinal OB fold, -strands 4 and 5 are linked by a crossover connection, leaving the fifth -strand at the interface between the N- and C-terminal domains. The C-terminal 10 makes a hydrogen bond to the 5, and thus all the -strands in the molecule are connected by hydrogen bonds.

10.1128/9781555818142/fig9-2_thmb.gif
10.1128/9781555818142/fig9-2.gif
Image of Figure 2
Figure 2

Topological diagram showing secondary structure of L2-RBD. The molecule consists of 10 -strands (indicated by arrows) and a short 3 helix (indicated by a rectangle). Unlike in the ordinal OB fold, -strands 4 and 5 are linked by a crossover connection, leaving the fifth -strand at the interface between the N- and C-terminal domains. The C-terminal 10 makes a hydrogen bond to the 5, and thus all the -strands in the molecule are connected by hydrogen bonds.

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
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Figure 3

Amino acid residues identified by mutagenesis experiments as essential for 23S rRNA binding. (Left) Positively charged residues important for 23S rRNA binding. Most of the residues that affect 23S rRNA binding are located in the Nterminal domain. The most important residues (Arg86 and Arg155) are located in the protruding loops of the N- and Cterminal domains, respectively. The side chains of these residues face the gate of the interface between two subdomains, a putative RNA binding site. (Right) Aromatic residues important for 23S rRNA binding. Phe66 and Tyr95 are at the interface between two subdomains, and Tyr102 is exposed to the molecular surface at the N-terminal extension of the molecule.

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Image of Figure 3
Figure 3

Amino acid residues identified by mutagenesis experiments as essential for 23S rRNA binding. (Left) Positively charged residues important for 23S rRNA binding. Most of the residues that affect 23S rRNA binding are located in the Nterminal domain. The most important residues (Arg86 and Arg155) are located in the protruding loops of the N- and Cterminal domains, respectively. The side chains of these residues face the gate of the interface between two subdomains, a putative RNA binding site. (Right) Aromatic residues important for 23S rRNA binding. Phe66 and Tyr95 are at the interface between two subdomains, and Tyr102 is exposed to the molecular surface at the N-terminal extension of the molecule.

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
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Figure 4

Comparison of the fold of N- and C-terminal subdomains of L2-RBD with those of other proteins having similar motifs. (Left) The SH3-like-barrel domain of the biotin biosynthetic operon repressor, BirA, C-terminal domain (1BIA). (Middle) L2-RBD. The N-terminal half of L2-RBD is an OB fold, and the C-terminal half is an SH3-like barrel. The fifth strand (5) is at the linker region between the OB fold and the SH3-like barrel. (Right) The OB fold of the S1 domain of the polynucleotide phosphorylase of (1SRO).

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Image of Figure 4
Figure 4

Comparison of the fold of N- and C-terminal subdomains of L2-RBD with those of other proteins having similar motifs. (Left) The SH3-like-barrel domain of the biotin biosynthetic operon repressor, BirA, C-terminal domain (1BIA). (Middle) L2-RBD. The N-terminal half of L2-RBD is an OB fold, and the C-terminal half is an SH3-like barrel. The fifth strand (5) is at the linker region between the OB fold and the SH3-like barrel. (Right) The OB fold of the S1 domain of the polynucleotide phosphorylase of (1SRO).

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
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Figure 5

Comparison of molecules that have OB-fold and SH3-like-barrel domains. (Left) L2-RBD. (Right) Eukaryotic translation initiation factor IF-5A (2EIF). The N-terminal domain of IF-5A is an SH3-like barrel, and the C-terminal domain is an OB fold, the reverse of the situation in the L2-RBD. The molecules are drawn in rainbow colors to show the chain connectivity clearly.

10.1128/9781555818142/fig9-5_thmb.gif
10.1128/9781555818142/fig9-5.gif
Image of Figure 5
Figure 5

Comparison of molecules that have OB-fold and SH3-like-barrel domains. (Left) L2-RBD. (Right) Eukaryotic translation initiation factor IF-5A (2EIF). The N-terminal domain of IF-5A is an SH3-like barrel, and the C-terminal domain is an OB fold, the reverse of the situation in the L2-RBD. The molecules are drawn in rainbow colors to show the chain connectivity clearly.

Citation: Tanaka I, Nakagawa A, Nakashima T, Taniguchi M, Hosaka H, Kimura M. 2000. Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, p 85-92. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch9
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