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A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.

Hsiao C, Williams LD - Nucleic Acids Res. (2009)

Bottom Line: The 2D elements of the 23S rRNA that are linked by Mg(2+)-muc's are conserved between the rRNAs of bacteria, archaea and eukarya and in mitochondrial rRNA, and in a proposed minimal 23S-rRNA.We observe Mg(2+)-muc's in other rRNAs including the bacterial 16S rRNA, and the P4-P6 domain of the tetrahymena Group I intron ribozyme.It appears that Mg(2+)-muc's are a primeval motif, with pivotal roles in RNA folding, function and evolution.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

ABSTRACT
The ribosome is an ancient macromolecular machine responsible for the synthesis of all proteins in all living organisms. Here we demonstrate that the ribosomal peptidyl transferase center (PTC) is supported by a framework of magnesium microclusters (Mg(2+)-muc's). Common features of Mg(2+)-muc's include two paired Mg(2+) ions that are chelated by a common bridging phosphate group in the form Mg((a))(2+)-(O1P-P-O2P)-Mg((b))(2+). This bridging phosphate is part of a 10-membered chelation ring in the form Mg((a))(2+)-(OP-P-O5'-C5'-C4'-C3'-O3'-P-OP)-Mg((a))(2+). The two phosphate groups of this 10-membered ring are contributed by adjacent residues along the RNA backbone. Both Mg(2+) ions are octahedrally coordinated, but are substantially dehydrated by interactions with additional RNA phosphate groups. The Mg(2+)-muc's in the LSU (large subunit) appear to be highly conserved over evolution, since they are unchanged in bacteria (Thermus thermophilus, PDB entry 2J01) and archaea (Haloarcula marismortui, PDB entry 1JJ2). The 2D elements of the 23S rRNA that are linked by Mg(2+)-muc's are conserved between the rRNAs of bacteria, archaea and eukarya and in mitochondrial rRNA, and in a proposed minimal 23S-rRNA. We observe Mg(2+)-muc's in other rRNAs including the bacterial 16S rRNA, and the P4-P6 domain of the tetrahymena Group I intron ribozyme. It appears that Mg(2+)-muc's are a primeval motif, with pivotal roles in RNA folding, function and evolution.

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The Mg2+-μc motif. (A) A schematic diagram illustrating the Mg2+(a)–(O1P-P-O2P)–Mg2+(b) bridge (outlined in blue), the 10-membered chelation ring (yellow), an unstacked base and the additional RNA phosphate groups that enter the Mg2+ first shell at variable positions. Carbon is green, oxygen is red and phosphorous is orange. Magnesium (a) is cyan while magnesium (b) is brown. (B) Superimposition of four Mg2+-μc's (D1 purple, D2 yellow, D3 gray and D4 green) from the H. marismortui LSU. All of the atoms shown here were used in the superimposition of the clusters except for the RNA bases.
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Figure 2: The Mg2+-μc motif. (A) A schematic diagram illustrating the Mg2+(a)–(O1P-P-O2P)–Mg2+(b) bridge (outlined in blue), the 10-membered chelation ring (yellow), an unstacked base and the additional RNA phosphate groups that enter the Mg2+ first shell at variable positions. Carbon is green, oxygen is red and phosphorous is orange. Magnesium (a) is cyan while magnesium (b) is brown. (B) Superimposition of four Mg2+-μc's (D1 purple, D2 yellow, D3 gray and D4 green) from the H. marismortui LSU. All of the atoms shown here were used in the superimposition of the clusters except for the RNA bases.

Mentions: The basic motif of the Mg2+-μc is defined by several features (Figure 2A). Two paired Mg2+ ions are chelated by a common bridging phosphate group in the form Mg2+(a)–(O1P-P-O2P)–Mg2+(b). This bridging phosphate is part of a 10-membered chelation ring in the form Mg2+(a)–(OP-P-O5′-C5′-C4′-C3′-O3′-P-OP)–Mg2+(a). The two phosphate groups of this 10-membered ring are contributed by adjacent residues along the RNA backbone. Both Mg2+ ions are octahedrally coordinated, but are substantially dehydrated by interactions with additional RNA phosphate groups.Figure 2.


A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.

Hsiao C, Williams LD - Nucleic Acids Res. (2009)

The Mg2+-μc motif. (A) A schematic diagram illustrating the Mg2+(a)–(O1P-P-O2P)–Mg2+(b) bridge (outlined in blue), the 10-membered chelation ring (yellow), an unstacked base and the additional RNA phosphate groups that enter the Mg2+ first shell at variable positions. Carbon is green, oxygen is red and phosphorous is orange. Magnesium (a) is cyan while magnesium (b) is brown. (B) Superimposition of four Mg2+-μc's (D1 purple, D2 yellow, D3 gray and D4 green) from the H. marismortui LSU. All of the atoms shown here were used in the superimposition of the clusters except for the RNA bases.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2691814&req=5

Figure 2: The Mg2+-μc motif. (A) A schematic diagram illustrating the Mg2+(a)–(O1P-P-O2P)–Mg2+(b) bridge (outlined in blue), the 10-membered chelation ring (yellow), an unstacked base and the additional RNA phosphate groups that enter the Mg2+ first shell at variable positions. Carbon is green, oxygen is red and phosphorous is orange. Magnesium (a) is cyan while magnesium (b) is brown. (B) Superimposition of four Mg2+-μc's (D1 purple, D2 yellow, D3 gray and D4 green) from the H. marismortui LSU. All of the atoms shown here were used in the superimposition of the clusters except for the RNA bases.
Mentions: The basic motif of the Mg2+-μc is defined by several features (Figure 2A). Two paired Mg2+ ions are chelated by a common bridging phosphate group in the form Mg2+(a)–(O1P-P-O2P)–Mg2+(b). This bridging phosphate is part of a 10-membered chelation ring in the form Mg2+(a)–(OP-P-O5′-C5′-C4′-C3′-O3′-P-OP)–Mg2+(a). The two phosphate groups of this 10-membered ring are contributed by adjacent residues along the RNA backbone. Both Mg2+ ions are octahedrally coordinated, but are substantially dehydrated by interactions with additional RNA phosphate groups.Figure 2.

Bottom Line: The 2D elements of the 23S rRNA that are linked by Mg(2+)-muc's are conserved between the rRNAs of bacteria, archaea and eukarya and in mitochondrial rRNA, and in a proposed minimal 23S-rRNA.We observe Mg(2+)-muc's in other rRNAs including the bacterial 16S rRNA, and the P4-P6 domain of the tetrahymena Group I intron ribozyme.It appears that Mg(2+)-muc's are a primeval motif, with pivotal roles in RNA folding, function and evolution.

View Article: PubMed Central - PubMed

Affiliation: School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.

ABSTRACT
The ribosome is an ancient macromolecular machine responsible for the synthesis of all proteins in all living organisms. Here we demonstrate that the ribosomal peptidyl transferase center (PTC) is supported by a framework of magnesium microclusters (Mg(2+)-muc's). Common features of Mg(2+)-muc's include two paired Mg(2+) ions that are chelated by a common bridging phosphate group in the form Mg((a))(2+)-(O1P-P-O2P)-Mg((b))(2+). This bridging phosphate is part of a 10-membered chelation ring in the form Mg((a))(2+)-(OP-P-O5'-C5'-C4'-C3'-O3'-P-OP)-Mg((a))(2+). The two phosphate groups of this 10-membered ring are contributed by adjacent residues along the RNA backbone. Both Mg(2+) ions are octahedrally coordinated, but are substantially dehydrated by interactions with additional RNA phosphate groups. The Mg(2+)-muc's in the LSU (large subunit) appear to be highly conserved over evolution, since they are unchanged in bacteria (Thermus thermophilus, PDB entry 2J01) and archaea (Haloarcula marismortui, PDB entry 1JJ2). The 2D elements of the 23S rRNA that are linked by Mg(2+)-muc's are conserved between the rRNAs of bacteria, archaea and eukarya and in mitochondrial rRNA, and in a proposed minimal 23S-rRNA. We observe Mg(2+)-muc's in other rRNAs including the bacterial 16S rRNA, and the P4-P6 domain of the tetrahymena Group I intron ribozyme. It appears that Mg(2+)-muc's are a primeval motif, with pivotal roles in RNA folding, function and evolution.

Show MeSH
Related in: MedlinePlus