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Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha.

Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D - Elife (2016)

Bottom Line: It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome.Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function.By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.

ABSTRACT
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.

No MeSH data available.


Related in: MedlinePlus

Analysis of the structural model of Drosophila Pur-alpha repeat III.Stereo view of the helical region of chain B (grey), from lysine 254 to proline 235 with (2Fo-Fc) electron-density map (blue).DOI:http://dx.doi.org/10.7554/eLife.11297.017
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fig4s1: Analysis of the structural model of Drosophila Pur-alpha repeat III.Stereo view of the helical region of chain B (grey), from lysine 254 to proline 235 with (2Fo-Fc) electron-density map (blue).DOI:http://dx.doi.org/10.7554/eLife.11297.017

Mentions: To understand the role of the third repeat of Pur-alpha (Figure 1A; Figure 1—figure supplement 1D) for DNA/RNA binding, we determined its crystal structure. Initial datasets were obtained from native crystals at 2.7 Å resolution, from which electron-density maps were calculated by molecular replacement with the apo-structures of Pur-alpha from Borrelia and Drosophila as search templates (PDB-IDs: 3NM7 and 3K44, respectively). The final structure model was obtained in the same way from selenomethionine-derivatized crystals at 2.6 Å resolution (Table 1; Figure 4A; Figure 4—figure supplement 1). The structure consisting of two repeat III molecules shows the same overall fold as repeat I-II with an RMSD of 1.5 Å, and only few differences in the amino acid composition of its putative nucleic-acid-binding surface (Figure 4A; Figure 2—figure supplement 4B).10.7554/eLife.11297.016Figure 4.Crystal structure of PUR repeat III and assessment of its weak nucleic-acid-binding and unwinding activity. 


Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha.

Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D - Elife (2016)

Analysis of the structural model of Drosophila Pur-alpha repeat III.Stereo view of the helical region of chain B (grey), from lysine 254 to proline 235 with (2Fo-Fc) electron-density map (blue).DOI:http://dx.doi.org/10.7554/eLife.11297.017
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764581&req=5

fig4s1: Analysis of the structural model of Drosophila Pur-alpha repeat III.Stereo view of the helical region of chain B (grey), from lysine 254 to proline 235 with (2Fo-Fc) electron-density map (blue).DOI:http://dx.doi.org/10.7554/eLife.11297.017
Mentions: To understand the role of the third repeat of Pur-alpha (Figure 1A; Figure 1—figure supplement 1D) for DNA/RNA binding, we determined its crystal structure. Initial datasets were obtained from native crystals at 2.7 Å resolution, from which electron-density maps were calculated by molecular replacement with the apo-structures of Pur-alpha from Borrelia and Drosophila as search templates (PDB-IDs: 3NM7 and 3K44, respectively). The final structure model was obtained in the same way from selenomethionine-derivatized crystals at 2.6 Å resolution (Table 1; Figure 4A; Figure 4—figure supplement 1). The structure consisting of two repeat III molecules shows the same overall fold as repeat I-II with an RMSD of 1.5 Å, and only few differences in the amino acid composition of its putative nucleic-acid-binding surface (Figure 4A; Figure 2—figure supplement 4B).10.7554/eLife.11297.016Figure 4.Crystal structure of PUR repeat III and assessment of its weak nucleic-acid-binding and unwinding activity. 

Bottom Line: It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome.Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function.By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.

ABSTRACT
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.

No MeSH data available.


Related in: MedlinePlus