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Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5391-400. doi: 10.1073/pnas.1515737112. Epub 2015 Sep 15.

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP.

Author information

1
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016;
2
Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065;
3
Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065;
4
Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065; New York Genome Center, New York, NY, 10013.
5
Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065; pateld@mskcc.org Alexander.Serganov@nyumc.org.
6
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016; pateld@mskcc.org Alexander.Serganov@nyumc.org.

Abstract

Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K(+)-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.

KEYWORDS:

FMRP; G-quadruplex; RGG box; RNA structure; fragile X syndrome

PMID:
26374839
PMCID:
PMC4593078
DOI:
10.1073/pnas.1515737112
[Indexed for MEDLINE]
Free PMC Article

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