From Proteopedia

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Introduction

Hrp1 is a polyadenylation factor found in Saccharomyces cervisiae (yeast) ^[1]. This protein recognizes and binds to an RNA sequence in the 3'UTR upstream from the cleavage site called the polyadenylation enhancement element (PEE) ^[1]. Upon binding to the RNA, Hrp1 helps recruit additional proteins necessary for the cleavage and polyadenylation of the RNA molecule ^[1]. The structure of the Hrp1-PEE complex reveals the mechanism by which Hrp1 is able to recognize and bind to its specific RNA sequence at the atomic level ^[1].

Structure

Hrp1 is a single strand RNA-binding protein composed of two RNP-type RNA-binding domains (RBDs) arranged in tandem with a typical ßαßßαß architecture ^[1]. The two RBDs have similar topolgies, both containing a central antiparallel four-stranded with two α-helices running across one face ^[1]. The two RBDs associate to form a deep and positively charged , which constitutes the binding site for the RNA molecule ^[1].

Figure 1: Cartoon representation of the Hrp1-PEE complex. The RNA is shown as a stick model and is colored by element. Notice the interface between the ß-sheets of Hrp1 and the RNA.

Hrp1-RNA Interactions

The interface between Hrp1 and its target RNA sequence is dominated by interactions between key aromatic residues and RNA bases ^[1]. Only six RNA bases, an repeat, act as the PEE and form specific contacts with Hrp1 ^[1]. Hydrophilic residues of Hrp1 provide base specificity through hydrogen bonding ^[1]. Most of the key residues that interact with the RNA can be found in the ß-sheet region of Hrp1; however, loops and the interdomain linker are also essential for Hrp1-RNA recognition ^[1]. Perhaps the most important Hrp1-RNA interaction is the (a conserved residue) ^[1]. In this case, Trp168 stacks on Ade4 and forms crucial base-specific hydrogen bonds ^[1]. It is also worth noting that a second Hrp1 residue is critical to holding Ade4 in place, , which interacts via hydrogen bond with the N1 of Ade4 ^[1]. A third contributor, , also stacks with Ura7 to aid in RNA recognition and binding ^[1].

Figure 2: Sequence logo for residues 167-169 of Hrp1. The logo displays the frequency of residues occuring at specific positions within Hrp1. W168 is always conserved in Hrp1 and RRMs of similar proteins.

RBD-RBD Interactions and the Linker Region

As mentioned above, Hrp1 is composed of two RBDs. The RBDs are connected by a linker region which also contains an crucial residue for RNA binding. Ile234 holds Ade6 stacked in place with Phe162 . Experimental evidence from the NMR data ^[1] suggests that the two RBDs act independently until binding the PEE. Binding the PEE causes the linker region to adopt a short helical structure to rigidly hold the . Aside from the linker helix, the only interaction between the RBDs is due to between Lys231 and Asp271.

Relevance

Relationships to other proteins

The RNP-type RBD is found in many proteins involved in post-transcriptional pre-mRNA processing (5' end capping, splicing, 3' end polyadenylation, and transport from the nucleus)^[2].

Interaction with RNA15

RNA15 is another RNA-binding protein (RBD) with a single N-terminal RNA recognition motif (RRM) ^[3] .

References

1. ↑ ^{1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15} Perez-Canadillas JM. Grabbing the message: structural basis of mRNA 3'UTR recognition by Hrp1. EMBO J. 2006 Jul 12;25(13):3167-78. Epub 2006 Jun 22. PMID:16794580
2. ↑ Clery A, Blatter M, Allain FH. RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol. 2008 Jun;18(3):290-8. doi: 10.1016/j.sbi.2008.04.002. PMID:18515081 doi:http://dx.doi.org/10.1016/j.sbi.2008.04.002
3. ↑ Leeper TC, Qu X, Lu C, Moore C, Varani G. Novel protein-protein contacts facilitate mRNA 3'-processing signal recognition by Rna15 and Hrp1. J Mol Biol. 2010 Aug 20;401(3):334-49. Epub 2010 Jun 19. PMID:20600122 doi:10.1016/j.jmb.2010.06.032

1. Pérez-Cañadillas, J. Grabbing The Message: Structural Basis Of Mrna 3′UTR Recognition By Hrp1. The EMBO Journal 2006, 25, 3167-3178. 2. Cléry, A.; Blatter, M.; Allain, F. RNA Recognition Motifs: Boring? Not Quite. Current Opinion in Structural Biology 2008, 18, 290-298. 3. Guo, Z.; Sherman, F. 3′-End-Forming Signals Of Yeast Mrna. Trends in Biochemical Sciences 1996, 21, 477-481. 4. Kessler, M.; Henry, M.; Shen, E.; Zhao, J.; Gross, S.; Silver, P.; Moore, C. Hrp1, A Sequence-Specific RNA-Binding Protein That Shuttles Between The Nucleus And The Cytoplasm, Is Required For Mrna 3'-End Formation In Yeast. Genes & Development 1997, 11, 2545-2556. 5. Leeper, T.; Qu, X.; Lu, C.; Moore, C.; Varani, G. Novel Protein–Protein Contacts Facilitate Mrna 3′-Processing Signal Recognition By Rna15 And Hrp1. Journal of Molecular Biology 2010, 401, 334-349. 6. The PyMol Molecular Graphics System, Version 2.0 Schrödinger, LLC. (for structural depictions)