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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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Four Mg2+-μc's are observed in the LSU of H. marismortui (PDB entry 1JJ2). (A) View into the Peptidyl Transfer Center. The four Mg2+-μc's are represented as solid surfaces. The RNA atoms lining the polypeptide exit tunnel are accented in black. Mg2+-μc's D1, D2 and D4 encircle the PTC. Mg2+-μc's are colored: D1, purple; D2, yellow; D3, gray; D4, green. Ribosomal proteins and the 5S rRNA are omitted for clarity. (B) This view, looking across the polypeptide exit tunnel, is rotated by 90° relative to that of panel A. (C) The secondary structures of LSU rRNAs of H. marismortui [23S rRNA (7), dashed black line] and the mitochondrion of B. taurus [16S rRNA (51), red line]. Phosphate groups that are linked by magnesium ions within Mg2+-μc's are indicated by broad colored lines. The secondary structural elements that interact with Mg2+-μc's are conserved in these widely divergent LSUs. In the C. elegans LSU (not shown), the rRNA that binds to D3 is absent (52). The question mark indicates the portion of the mitochondrial B. Taurus LSU rRNA for which the secondary structure is unknown.
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Figure 1: Four Mg2+-μc's are observed in the LSU of H. marismortui (PDB entry 1JJ2). (A) View into the Peptidyl Transfer Center. The four Mg2+-μc's are represented as solid surfaces. The RNA atoms lining the polypeptide exit tunnel are accented in black. Mg2+-μc's D1, D2 and D4 encircle the PTC. Mg2+-μc's are colored: D1, purple; D2, yellow; D3, gray; D4, green. Ribosomal proteins and the 5S rRNA are omitted for clarity. (B) This view, looking across the polypeptide exit tunnel, is rotated by 90° relative to that of panel A. (C) The secondary structures of LSU rRNAs of H. marismortui [23S rRNA (7), dashed black line] and the mitochondrion of B. taurus [16S rRNA (51), red line]. Phosphate groups that are linked by magnesium ions within Mg2+-μc's are indicated by broad colored lines. The secondary structural elements that interact with Mg2+-μc's are conserved in these widely divergent LSUs. In the C. elegans LSU (not shown), the rRNA that binds to D3 is absent (52). The question mark indicates the portion of the mitochondrial B. Taurus LSU rRNA for which the secondary structure is unknown.

Mentions: Chelation effects and topology influence interactions of nucleic acids with ions. For example magnesium forms a mononuclear motif with ADP/ATP in which one Mg2+ ion is chelated by a six-membered ring consisting of atoms Mg2+(a)–OαP-P-O-P-OβP–Mg2+(a) (18). Here we observe that a framework of dinuclear magnesium complexes Mg2+(a)–RNA–Mg2+(b) flanks the peptidyl transferase center (PTC) in LSU ribosomal structures (Figure 1). In these dinuclear clusters, two Mg2+ ions are chelated by a common bridging phosphate group. Additional structural features are conserved among these clusters, which are also identified in other RNAs, indicating that dinuclear RNA magnesium clusters compose by distinctive yet recurrent motif. This dinuclear Mg2+(a)–RNA–Mg2+(b) motif is referred to here as the magnesium microcluster (Mg2+-μc).Figure 1.


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

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

Four Mg2+-μc's are observed in the LSU of H. marismortui (PDB entry 1JJ2). (A) View into the Peptidyl Transfer Center. The four Mg2+-μc's are represented as solid surfaces. The RNA atoms lining the polypeptide exit tunnel are accented in black. Mg2+-μc's D1, D2 and D4 encircle the PTC. Mg2+-μc's are colored: D1, purple; D2, yellow; D3, gray; D4, green. Ribosomal proteins and the 5S rRNA are omitted for clarity. (B) This view, looking across the polypeptide exit tunnel, is rotated by 90° relative to that of panel A. (C) The secondary structures of LSU rRNAs of H. marismortui [23S rRNA (7), dashed black line] and the mitochondrion of B. taurus [16S rRNA (51), red line]. Phosphate groups that are linked by magnesium ions within Mg2+-μc's are indicated by broad colored lines. The secondary structural elements that interact with Mg2+-μc's are conserved in these widely divergent LSUs. In the C. elegans LSU (not shown), the rRNA that binds to D3 is absent (52). The question mark indicates the portion of the mitochondrial B. Taurus LSU rRNA for which the secondary structure is unknown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2691814&req=5

Figure 1: Four Mg2+-μc's are observed in the LSU of H. marismortui (PDB entry 1JJ2). (A) View into the Peptidyl Transfer Center. The four Mg2+-μc's are represented as solid surfaces. The RNA atoms lining the polypeptide exit tunnel are accented in black. Mg2+-μc's D1, D2 and D4 encircle the PTC. Mg2+-μc's are colored: D1, purple; D2, yellow; D3, gray; D4, green. Ribosomal proteins and the 5S rRNA are omitted for clarity. (B) This view, looking across the polypeptide exit tunnel, is rotated by 90° relative to that of panel A. (C) The secondary structures of LSU rRNAs of H. marismortui [23S rRNA (7), dashed black line] and the mitochondrion of B. taurus [16S rRNA (51), red line]. Phosphate groups that are linked by magnesium ions within Mg2+-μc's are indicated by broad colored lines. The secondary structural elements that interact with Mg2+-μc's are conserved in these widely divergent LSUs. In the C. elegans LSU (not shown), the rRNA that binds to D3 is absent (52). The question mark indicates the portion of the mitochondrial B. Taurus LSU rRNA for which the secondary structure is unknown.
Mentions: Chelation effects and topology influence interactions of nucleic acids with ions. For example magnesium forms a mononuclear motif with ADP/ATP in which one Mg2+ ion is chelated by a six-membered ring consisting of atoms Mg2+(a)–OαP-P-O-P-OβP–Mg2+(a) (18). Here we observe that a framework of dinuclear magnesium complexes Mg2+(a)–RNA–Mg2+(b) flanks the peptidyl transferase center (PTC) in LSU ribosomal structures (Figure 1). In these dinuclear clusters, two Mg2+ ions are chelated by a common bridging phosphate group. Additional structural features are conserved among these clusters, which are also identified in other RNAs, indicating that dinuclear RNA magnesium clusters compose by distinctive yet recurrent motif. This dinuclear Mg2+(a)–RNA–Mg2+(b) motif is referred to here as the magnesium microcluster (Mg2+-μc).Figure 1.

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