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From Proteopedia

Structure of FMRP

Predicted FMRP

Fragile X messenger ribonucleoprotein (FMRP) is encoded by the fragile X messenger ribonucleoprotein 1 (FMR1) gene, located in the X chromosome, and is associated with the fragile X syndrome (FXS), Fragile X Tremor/Ataxia Syndrome (FXTAS), and Premature Ovarian Failure (POF1). FMRP functions as a synaptic regulator by binding to mRNAs and inhibiting its translation, therefore regulating the synthesis of proteins in the synapse. It is also an RNA binding protein, which is responsible for the transportation of mRNAs to the cytoplasm. The FMRP can also bind to its own FMR1 transcripts, possibly as a self-regulatory mechanism.

The FMRP is highly expressed in neurons and genitalia, and it's located mostly in the cytoplasm and at lower levels in the nucleus. It contains domains related to its RNA-binding function, either in the N-terminal or C-terminal regions; the Agenet and the KH0-domains are located in the N-terminal region, and they, respectively, exerce functions in binding to methylated lysin and RNA binding; the KH1 and KH2 motifs are located in the central region of the protein; and the RGG box, in the C-terminal region, acting as a binding to RNA, specifically to G-quadruplexes, a secondary RNA structure. The KH1, KH2, and RGG box domains allow the FMRP to bind and translate a number of mRNAs related to synaptic plasticity. ^[1]

The protein has 20 non-redundant isoforms and the most common is isoform 7, and the longest isoform contains 632 aminoacids. ^[2].

The predicted image was generated from Ensembl, by the AlphaFold program.

Overall structure

N-terminal domain of the FMRP (PDB entry 4QVZ)

Drag the structure with the mouse to rotate

1 N-terminal domain
2 Central portion
3 RGG motif
4 Associated diseases
5 References

N-terminal domain

The N-terminal domain (NTD) of the FMRP is the first 215 aminoacids of the protein, containing two in tandem Agenet domains and one KH domain. The NTD is important for the functions of the protein as a RBP and its participation in the ribonucleoprotein (RNP) complex.

The NTD was shown to adopt independent folding, and its tertiary structure was found to be compatible with two tandem . Both of the Agenet domains resemble those of Argonaute, a protein involved in RNA interference, as they resemble structuraly Tudor domains, it is possible to assume functional similarities between them.

The characterize the Agenet domain and its structure, and there is a , highlighted in magenta, between the beta sheets of the Agenet 1 and Agenet 2, connecting them.

It's been shown that, when the FMRP is in the nucleus, the Agenet domain allows the FMRP to interact with the chromatin and regulate the DNA damage response.

And has also been demonstrated that the Agenet domains bind to methylated lysine, supporting the histone binding function of the FMRP due to its aromatic cage in the structure; specifically, the Agenet motif 2 binds to trimethylated lysine. The highlighted in red are part of the Agenet 1 and the ones highlighted in blue are part of the Agenet 2 domain related to the recognition of methylated lysine, as they all have aromatic cages with the potential for this binding.

^[3].

The K-homology domain (KH domain) folding is similar to other RBPs domains, which play an important role in RNA binding and protein-protein interactions.

Here is the highlighted in red. Many RNA-binding proteins contain the KH motif, a conserved RNA-binding domain, but different from the KH1 and KH2 motifs, which contain a G-X-X-G canonical motif, that will be explained in further details in the next topic, instead this one has an . It is most likely involved in RNA binding and regulation, as seen in other proteins that also contain KH motifs. To give a more thorough response addressing the precise role played by the KH theme in FMRP, additional details would be needed.

Overall, the FMRP NTD plays an important role as an RNA-binding protein, and its involvement in RNP complexes and its specific domains and motifs allow it to bind to specific RNAs and regulate their translation. ^[4]

The 3D structure of the N-terminal domain was obtained by X-ray diffraction with a 3.19 Å resolution and expressed in E. coli.

Central portion

The central portion of the protein contains the in tandem . The type of KH domains in eukaryots is type 1 fold, in which a , and they both have a canonical (glycine followed by any two aminoacids and another glycine) conserved domain, highlighted in magenta, connecting the central helices of the domain and a variable loop. There is a gap in the KH motif, which can hold four nucleic acid bases; it happens when an alpha-helix 1, alpha-helix 2, a GXXG on the left, and a variable loop are present in the domain, in the case of the FMRP, another beta-sheet. This helps the FMRP in its RBP function, as they are motifs that are related to RNA or ssDNA binding. ^[5]

RGG motif

An important motif of the FMRP is the , which the protein uses to bind to guanine G-quadruplexes, a structure that consists of nucleic acid folding in which four guanines arrange in a planar conformation stabilized by Hoogsteen-type hydrogen bonds, named tetrad, and they are stabilized by a K+ cation (green ball in the image). The RNA being represented is the sc1 RNA, and the interaction between them was visualized through NMR. There are in the sc1 RNA. FMRP RGG motifs seem to prefer binding to specific structures.

Different domains and motifs mediate the RNA binding mechanism, and the exon 15-encoded (arginine - glycine - glycine) and the binding of FMRP to G-rich RNAs in vitro requires only the RGG motif, which occurs through the binding of a hydrogen bond between an RNA base and a aminoacid residue. The FMRP RGG motif is located in the C-terminal region of the protein and is well conserved in vertebrates. Crystal structure of the complex between the human FMRP RGG motif and G-quadruplex RNA The RGG motif binds to G-quadruplexes when it adopts a sharp turn and specifically binds to guanines from two consecutive G-C base pairs in the duplex-quadruplex junction. Several tetrads can stack in a single G-quadruplex structure and be stabilized further by potassium cations, in the case of FMRP targets, whereas they are destabilized by lithium cations.

The regulation of particular mRNAs and the binding of FMRP with ribosomes and proteins depend on this interaction between the RGG motif and G-quadruplex RNA.

Therefore, understanding the interaction RGG-RNA is important for the comprehension of FMRP and FXS. The structure being represented on the right represents the FMRP RGG motif and the G-quadruplex secondary structure in the RNA.

The protein structure was obtained by X-ray diffraction with a resolution of 3 Å. ^[6]

Associated diseases

Trinucleotides repeats (CGG) are located in CpG islands in the 5' untranslated region (UTR) of the gene related to the expression of the gene. Individuals carrying up to 44 repeats of trinucleotides are of common aleles. Individuals that have between 44 and 55 repeats are known to carry the premutation, usually associated with FXTAS and PFO1. However, when the repeat expansion is above 55 the individual is carrying the full mutation, which leads to the silencing of the gene, due to methylation, therefore there is absence or reduced levels of the FMRP, causing abnormal synaptic development and symptons associated with the FXS.

References

↑ SUARDI, G. A. M.; HADDAD, L. A. Chapter Three - FMRP ribonucleoprotein complexes and RNA homeostasis.[1]
↑ Hu, Y., Chen, Z., Fu, Y., He, Q., Jiang, L., Zheng, J., Gao, Y., Mei, P., Chen, Z. and Ren, X. (2015). The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers. Nature Communications, [online] 6(1), p.6634. [2]
↑ MYRICK, L. K. et al. Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. Human Molecular Genetics, v. 24, n. 6, p. 1733–1740, 20 nov. 2014.[3]
↑ MYRICK, L. K. et al. Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. Human Molecular Genetics, v. 24, n. 6, p. 1733–1740, 20 nov. 2014.[4]
↑ Valverde, R., Edwards, L. and Regan, L. (2008). Structure and function of KH domains. FEBS Journal, 275(11), pp.2712–2726. [5]
↑ VASILYEV, N. et al. Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proceedings of the National Academy of Sciences, v. 112, n. 39, p. E5391–E5400, 15 set. 2015.[6]