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Structural basis for the dual RNA-recognition modes of human Tra2-β RRM.

Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Güntert P, Yokoyama S, Muto Y - Nucleic Acids Res. (2010)

Bottom Line: We then solved the complex structure of the hTra2-β RRM with the (GAA)(2) sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the β-sheet surface.Further NMR experiments revealed that the hTra2-β RRM recognizes the CAA sequence when it is integrated in the stem-loop structure.This study indicates that the hTra2-β RRM recognizes two types of RNA sequences in different RNA binding modes.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Systems and Structural Biology Center, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

ABSTRACT
Human Transformer2-β (hTra2-β) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2-β specifically binds to two types of RNA sequences [the CAA and (GAA)(2) sequences]. We determined the solution structure of the hTra2-β RRM (spanning residues Asn110-Thr201), which not only has a canonical RRM fold, but also an unusual alignment of the aromatic amino acids on the β-sheet surface. We then solved the complex structure of the hTra2-β RRM with the (GAA)(2) sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the β-sheet surface. Further NMR experiments revealed that the hTra2-β RRM recognizes the CAA sequence when it is integrated in the stem-loop structure. This study indicates that the hTra2-β RRM recognizes two types of RNA sequences in different RNA binding modes.

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Comparison between the Nup35 RRM (PDBID: 1WWH) (A), the hTra2-β RRM (B) and the RBMY RRM (PDBID: 2FY1) (C). Top panel: Schematic representation of the amino acids on the β-sheet surface for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. Solvent-exposed amino acids are colored black, glycine residues are cyan, and aromatic amino acids are green or magenta. Amino acids involved in the core formation are indicated by faint colors. Middle panel: Ribbon representations of the tertiary structures of the homodimerized Nup35 RRM, the hTra2-β RRM in complex with [5′-(GAAGAA)-3′], and the RBMY RRM in complex with the target RNA molecule. Bottom panel: Close-up view of the interaction site on the β-sheet surface with the target molecules for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. The aromatic side chains, colored green or magenta in the top panel, are shown on the tertiary structures in the middle and bottom panels.
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Figure 7: Comparison between the Nup35 RRM (PDBID: 1WWH) (A), the hTra2-β RRM (B) and the RBMY RRM (PDBID: 2FY1) (C). Top panel: Schematic representation of the amino acids on the β-sheet surface for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. Solvent-exposed amino acids are colored black, glycine residues are cyan, and aromatic amino acids are green or magenta. Amino acids involved in the core formation are indicated by faint colors. Middle panel: Ribbon representations of the tertiary structures of the homodimerized Nup35 RRM, the hTra2-β RRM in complex with [5′-(GAAGAA)-3′], and the RBMY RRM in complex with the target RNA molecule. Bottom panel: Close-up view of the interaction site on the β-sheet surface with the target molecules for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. The aromatic side chains, colored green or magenta in the top panel, are shown on the tertiary structures in the middle and bottom panels.

Mentions: In the case of the hTra2-β RRM, the alignment of the aromatic amino acid residues (Phe123, Phe161, Phe163 and Tyr165) on the β-sheet surface is unusual, as compared to that in the canonical RRMs, and the amino-acid sequence of the β1 strand (RNP2) is distinct from the consensus RNP2 sequence (Figure 7B, top). In the canonical RRM, the second position of the β1 strand is occupied by an aromatic amino acid residue, and the fourth position contains a small amino acid residue, such as Gly (as a representative canonical RRM, the RRM of the RNA binding motif Y (RBMY) protein is shown in Figure 7C, top). In contrast, in the hTra2-β RRM, the second and fourth positions are occupied by Gly121 and Phe123, respectively (Figure 7B, top).Figure 7.


Structural basis for the dual RNA-recognition modes of human Tra2-β RRM.

Tsuda K, Someya T, Kuwasako K, Takahashi M, He F, Unzai S, Inoue M, Harada T, Watanabe S, Terada T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A, Sugano S, Güntert P, Yokoyama S, Muto Y - Nucleic Acids Res. (2010)

Comparison between the Nup35 RRM (PDBID: 1WWH) (A), the hTra2-β RRM (B) and the RBMY RRM (PDBID: 2FY1) (C). Top panel: Schematic representation of the amino acids on the β-sheet surface for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. Solvent-exposed amino acids are colored black, glycine residues are cyan, and aromatic amino acids are green or magenta. Amino acids involved in the core formation are indicated by faint colors. Middle panel: Ribbon representations of the tertiary structures of the homodimerized Nup35 RRM, the hTra2-β RRM in complex with [5′-(GAAGAA)-3′], and the RBMY RRM in complex with the target RNA molecule. Bottom panel: Close-up view of the interaction site on the β-sheet surface with the target molecules for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. The aromatic side chains, colored green or magenta in the top panel, are shown on the tertiary structures in the middle and bottom panels.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3045587&req=5

Figure 7: Comparison between the Nup35 RRM (PDBID: 1WWH) (A), the hTra2-β RRM (B) and the RBMY RRM (PDBID: 2FY1) (C). Top panel: Schematic representation of the amino acids on the β-sheet surface for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. Solvent-exposed amino acids are colored black, glycine residues are cyan, and aromatic amino acids are green or magenta. Amino acids involved in the core formation are indicated by faint colors. Middle panel: Ribbon representations of the tertiary structures of the homodimerized Nup35 RRM, the hTra2-β RRM in complex with [5′-(GAAGAA)-3′], and the RBMY RRM in complex with the target RNA molecule. Bottom panel: Close-up view of the interaction site on the β-sheet surface with the target molecules for the Nup35 RRM, the hTra2-β RRM and the RBMY RRM. The aromatic side chains, colored green or magenta in the top panel, are shown on the tertiary structures in the middle and bottom panels.
Mentions: In the case of the hTra2-β RRM, the alignment of the aromatic amino acid residues (Phe123, Phe161, Phe163 and Tyr165) on the β-sheet surface is unusual, as compared to that in the canonical RRMs, and the amino-acid sequence of the β1 strand (RNP2) is distinct from the consensus RNP2 sequence (Figure 7B, top). In the canonical RRM, the second position of the β1 strand is occupied by an aromatic amino acid residue, and the fourth position contains a small amino acid residue, such as Gly (as a representative canonical RRM, the RRM of the RNA binding motif Y (RBMY) protein is shown in Figure 7C, top). In contrast, in the hTra2-β RRM, the second and fourth positions are occupied by Gly121 and Phe123, respectively (Figure 7B, top).Figure 7.

Bottom Line: We then solved the complex structure of the hTra2-β RRM with the (GAA)(2) sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the β-sheet surface.Further NMR experiments revealed that the hTra2-β RRM recognizes the CAA sequence when it is integrated in the stem-loop structure.This study indicates that the hTra2-β RRM recognizes two types of RNA sequences in different RNA binding modes.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Systems and Structural Biology Center, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

ABSTRACT
Human Transformer2-β (hTra2-β) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2-β specifically binds to two types of RNA sequences [the CAA and (GAA)(2) sequences]. We determined the solution structure of the hTra2-β RRM (spanning residues Asn110-Thr201), which not only has a canonical RRM fold, but also an unusual alignment of the aromatic amino acids on the β-sheet surface. We then solved the complex structure of the hTra2-β RRM with the (GAA)(2) sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the β-sheet surface. Further NMR experiments revealed that the hTra2-β RRM recognizes the CAA sequence when it is integrated in the stem-loop structure. This study indicates that the hTra2-β RRM recognizes two types of RNA sequences in different RNA binding modes.

Show MeSH
Related in: MedlinePlus