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Category: Microbial Genetics and Molecular Biology
Structure and Evolution of the 23S rRNA Binding Domain of Protein L2, Page 1 of 2
< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555818142/9781555811846_Chap09-1.gif /docserver/preview/fulltext/10.1128/9781555818142/9781555811846_Chap09-2.gifAbstract:
This chapter focuses on the crystal structure of the RNA binding domain of BstL2, 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 Thermus aquaticus 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.
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Stereo view of BstL2-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 β-strand and a 310 helix (H1) connect two subdomains.
Stereo view of BstL2-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 β-strand and a 310 helix (H1) connect two subdomains.
Topological diagram showing secondary structure of BstL2-RBD. The molecule consists of 10 β-strands (indicated by arrows) and a short 310 helix (indicated by a rectangle). Unlike in the ordinal OB fold, β-strands 4 and 5 are linked by a crossover connection, leaving the fifth β-strand at the interface between the N- and C-terminal domains. The C-terminal β10 makes a hydrogen bond to the β5, and thus all the β-strands in the molecule are connected by hydrogen bonds.
Topological diagram showing secondary structure of BstL2-RBD. The molecule consists of 10 β-strands (indicated by arrows) and a short 310 helix (indicated by a rectangle). Unlike in the ordinal OB fold, β-strands 4 and 5 are linked by a crossover connection, leaving the fifth β-strand at the interface between the N- and C-terminal domains. The C-terminal β10 makes a hydrogen bond to the β5, and thus all the β-strands in the molecule are connected by hydrogen bonds.
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.
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.
Comparison of the fold of N- and C-terminal subdomains of BstL2-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) BstL2-RBD. The N-terminal half of BstL2-RBD is an OB fold, and the C-terminal half is an SH3-like barrel. The fifth strand (β5) 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 E. coli (1SRO).
Comparison of the fold of N- and C-terminal subdomains of BstL2-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) BstL2-RBD. The N-terminal half of BstL2-RBD is an OB fold, and the C-terminal half is an SH3-like barrel. The fifth strand (β5) 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 E. coli (1SRO).
Comparison of molecules that have OB-fold and SH3-like-barrel domains. (Left) BstL2-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 BstL2-RBD. The molecules are drawn in rainbow colors to show the chain connectivity clearly.
Comparison of molecules that have OB-fold and SH3-like-barrel domains. (Left) BstL2-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 BstL2-RBD. The molecules are drawn in rainbow colors to show the chain connectivity clearly.