Nuclear polyadenylated RNA-binding protein

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As mentioned above, Hrp1 is composed of two RBDs. The RBDs are connected by a <scene name='78/783765/Linker/3'>linker region</scene> (a short two-turn α-helix) which also contains an crucial residue for RNA binding. Ile234 holds Ade6 stacked in place with Phe162 <scene name='78/781945/Linker_rna/1'>via van der Waals contacts</scene>. Experimental evidence from the NMR data <ref name="GM3H"/> suggests that the two RBDs at independently until binding the PEE. Binding the PEE causes the linker region to adopt a short helical structure to rigidly hold the <scene name='78/781945/Protein_domains/2'>RBDs in place relative to each other</scene>. Aside from the linker helix, the only interaction between the RBDs is due to <scene name='78/781945/Interaction_between_domains/5'>a single salt bridge</scene> between Lys231 and Asp271 <ref name="GM3H"/>.
As mentioned above, Hrp1 is composed of two RBDs. The RBDs are connected by a <scene name='78/783765/Linker/3'>linker region</scene> (a short two-turn α-helix) which also contains an crucial residue for RNA binding. Ile234 holds Ade6 stacked in place with Phe162 <scene name='78/781945/Linker_rna/1'>via van der Waals contacts</scene>. Experimental evidence from the NMR data <ref name="GM3H"/> suggests that the two RBDs at independently until binding the PEE. Binding the PEE causes the linker region to adopt a short helical structure to rigidly hold the <scene name='78/781945/Protein_domains/2'>RBDs in place relative to each other</scene>. Aside from the linker helix, the only interaction between the RBDs is due to <scene name='78/781945/Interaction_between_domains/5'>a single salt bridge</scene> between Lys231 and Asp271 <ref name="GM3H"/>.
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=Interaction with RNA15=
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[[Image:Hrp1-RNA15.png|200 px|left|thumb|Figure 3: Interaction between Hrp1 (red), RNA15 (green) and RNA (blue).]]
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RNA15 is another RNA-binding protein with a single N-terminal RNA recognition motif (RRM) <ref name="RNA15">PMID: 20600122</ref>. RNA15 recognizes an A-rich positioning element (PE) downstream from the PEE but upstream from the 3' cleavage site <ref name="RNA15"/>. The recognition of the PE by RNA15 is crucial for precise cleavage of the RNA molecule. Hrp1 and RNA15 are held together by a separate protein, RNA14 <ref name="RNA15"/>. These proteins act together to anchor the polyadenylation and cleavage protein machinery relative to the cleavage site for precise 3'-end processing <ref name="RNA15"/>.
=Relationship to other proteins=
=Relationship to other proteins=
The RNP-type RBD is found in many proteins involved in post-transcriptional [https://en.wikipedia.org/wiki/Post-transcriptional_modification pre-mRNA processing] (5'-end capping, splicing, 3'-end cleavage and polyadenylation, and transport from the nucleus)<ref name="RRMB">PMID: 18515081</ref>. The unique RBD of Hrp1 enables the protein to bind an RNA sequence that differs in both length and content from the RNA sequences of other RNA-binding and mRNA processing proteins such as [http://proteopedia.org/wiki/index.php/2sxl sex lethal], [https://en.wikipedia.org/wiki/Poly(A)-binding_protein Poly (A)-binding protein (PABP)], and [http://proteopedia.org/wiki/index.php/1fxl HuD] <ref name="GM3H"/>. Like Hrp1, each of these proteins belong to the class of single strand proteins composed of two canonical RBDs; however, these proteins are differentiated by their target RNA sequence, their interactions with RNA at the atomic level, and their interdomain contacts <ref name="GM3H"/>. One way in which Hrp1 differentiates itself from these other proteins is by the fact that Hud, sex lethal, and PABP all contain at least one intra-RNA base-base stacking interaction, a feature that is not found in the Hrp1-PEE complex <ref name="GM3H"/>. It is possible that the intra-RNA interactions found in these other proteins is replaced by the crucial Trp168-Ade4 stacking interaction found in the Hrp1 complex <ref name="GM3H"/>. The fact that the intra-RNA base-base stacking interactions are replaced by the Trp168-Ade4 in the Hrp1-PEE complex might also explain why the Hrp1-RNA interface involves only 6 nucleotides whereas PABP, sex lethal, and HuD require a longer 8-10 nucleotide sequence in the RNA binding pocket <ref name="GM3H"/>.
The RNP-type RBD is found in many proteins involved in post-transcriptional [https://en.wikipedia.org/wiki/Post-transcriptional_modification pre-mRNA processing] (5'-end capping, splicing, 3'-end cleavage and polyadenylation, and transport from the nucleus)<ref name="RRMB">PMID: 18515081</ref>. The unique RBD of Hrp1 enables the protein to bind an RNA sequence that differs in both length and content from the RNA sequences of other RNA-binding and mRNA processing proteins such as [http://proteopedia.org/wiki/index.php/2sxl sex lethal], [https://en.wikipedia.org/wiki/Poly(A)-binding_protein Poly (A)-binding protein (PABP)], and [http://proteopedia.org/wiki/index.php/1fxl HuD] <ref name="GM3H"/>. Like Hrp1, each of these proteins belong to the class of single strand proteins composed of two canonical RBDs; however, these proteins are differentiated by their target RNA sequence, their interactions with RNA at the atomic level, and their interdomain contacts <ref name="GM3H"/>. One way in which Hrp1 differentiates itself from these other proteins is by the fact that Hud, sex lethal, and PABP all contain at least one intra-RNA base-base stacking interaction, a feature that is not found in the Hrp1-PEE complex <ref name="GM3H"/>. It is possible that the intra-RNA interactions found in these other proteins is replaced by the crucial Trp168-Ade4 stacking interaction found in the Hrp1 complex <ref name="GM3H"/>. The fact that the intra-RNA base-base stacking interactions are replaced by the Trp168-Ade4 in the Hrp1-PEE complex might also explain why the Hrp1-RNA interface involves only 6 nucleotides whereas PABP, sex lethal, and HuD require a longer 8-10 nucleotide sequence in the RNA binding pocket <ref name="GM3H"/>.
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=Interaction with RNA15=
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[[Image:Hrp1-RNA15.png|200 px|left|thumb|Figure 3: Interaction between Hrp1 (red), RNA15 (green) and RNA (blue).]]
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RNA15 is another RNA-binding protein with a single N-terminal RNA recognition motif (RRM) <ref name="RNA15">PMID: 20600122</ref>. RNA15 recognizes an A-rich positioning element (PE) downstream from the PEE but upstream from the 3' cleavage site <ref name="RNA15"/>. The recognition of the PE by RNA15 is crucial for precise cleavage of the RNA molecule. Hrp1 and RNA15 are held together by a separate protein, RNA14 <ref name="RNA15"/>. These proteins act together to anchor the polyadenylation and cleavage protein machinery relative to the cleavage site for precise 3'-end processing <ref name="RNA15"/>.
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=References=
=References=
<references/>
<references/>

Revision as of 01:10, 30 March 2018

Contents

Introduction

Hrp1

Drag the structure with the mouse to rotate

Hrp1 is a polyadenylation factor found in Saccharomyces cervisiae (yeast) [1]. This protein recognizes and binds to an RNA sequence in the 3'UTR of the messenger RNA (mRNA) 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 unique structural features 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.
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 nucleobases [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.
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 (a short two-turn α-helix) 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 at 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 [1].

Interaction with RNA15

Figure 3: Interaction between Hrp1 (red), RNA15 (green) and RNA (blue).
Figure 3: Interaction between Hrp1 (red), RNA15 (green) and RNA (blue).

RNA15 is another RNA-binding protein with a single N-terminal RNA recognition motif (RRM) [2]. RNA15 recognizes an A-rich positioning element (PE) downstream from the PEE but upstream from the 3' cleavage site [2]. The recognition of the PE by RNA15 is crucial for precise cleavage of the RNA molecule. Hrp1 and RNA15 are held together by a separate protein, RNA14 [2]. These proteins act together to anchor the polyadenylation and cleavage protein machinery relative to the cleavage site for precise 3'-end processing [2].

Relationship 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 cleavage and polyadenylation, and transport from the nucleus)[3]. The unique RBD of Hrp1 enables the protein to bind an RNA sequence that differs in both length and content from the RNA sequences of other RNA-binding and mRNA processing proteins such as sex lethal, Poly (A)-binding protein (PABP), and HuD [1]. Like Hrp1, each of these proteins belong to the class of single strand proteins composed of two canonical RBDs; however, these proteins are differentiated by their target RNA sequence, their interactions with RNA at the atomic level, and their interdomain contacts [1]. One way in which Hrp1 differentiates itself from these other proteins is by the fact that Hud, sex lethal, and PABP all contain at least one intra-RNA base-base stacking interaction, a feature that is not found in the Hrp1-PEE complex [1]. It is possible that the intra-RNA interactions found in these other proteins is replaced by the crucial Trp168-Ade4 stacking interaction found in the Hrp1 complex [1]. The fact that the intra-RNA base-base stacking interactions are replaced by the Trp168-Ade4 in the Hrp1-PEE complex might also explain why the Hrp1-RNA interface involves only 6 nucleotides whereas PABP, sex lethal, and HuD require a longer 8-10 nucleotide sequence in the RNA binding pocket [1].


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 1.16 1.17 1.18 1.19 1.20 1.21 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. ↑ 2.0 2.1 2.2 2.3 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
  3. ↑ 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
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