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The carboxy-terminal domain of Erb1 is a seven-bladed ß-propeller that binds RNA.

Wegrecki M, Marcin W, Neira JL, Bravo J - PLoS ONE (2015)

Bottom Line: This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat.The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding.Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, c/ Jaime Roig 11, 46010 Valencia, Spain.

ABSTRACT
Erb1 (Eukaryotic Ribosome Biogenesis 1) protein is essential for the maturation of the ribosomal 60S subunit. Functional studies in yeast and mammalian cells showed that altogether with Nop7 and Ytm1 it forms a stable subcomplex called PeBoW that is crucial for a correct rRNA processing. The exact function of the protein within the process remains unknown. The N-terminal region of the protein includes a well conserved region shown to be involved in PeBoW complex formation whereas the carboxy-terminal half was predicted to contain seven WD40 repeats. This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat. We performed analysis of molecular surface and crystal packing, together with multiple sequence alignment and comparison of the structure with other β-propellers, in order to identify areas that are more likely to mediate protein-protein interactions. The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding. Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis.

No MeSH data available.


Related in: MedlinePlus

Summary of the areas of Erb1Ct that are more likely to mediate protein-protein or protein-RNA interactions.The region corresponding to the conserved hot-spot residues is shown in green, the positively charged stretch of amino acids that might interact with RNA is highlighted in magenta, navy blue and red areas correspond to the conserved parts of the domain that establish important crystal contacts with symmetrically related molecules.
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pone.0123463.g009: Summary of the areas of Erb1Ct that are more likely to mediate protein-protein or protein-RNA interactions.The region corresponding to the conserved hot-spot residues is shown in green, the positively charged stretch of amino acids that might interact with RNA is highlighted in magenta, navy blue and red areas correspond to the conserved parts of the domain that establish important crystal contacts with symmetrically related molecules.

Mentions: Recently, it has been postulated that the WD40 proteins can also establish interactions by additional extensions or insertions that can occur between blades of the propeller [47]. It could be valid for Erb1 because, as we show here, it contains a long region that is introduced into WD2 and forms two visible α-helices and an additional strand. Residues in the propeller, outside the insertion, can contribute to the folding of the observed secondary motifs in this area. While the extra strand in blade 2 is probably necessary for structural stability of the inserted region and the propeller, the helices form an important protrusion that could serve as recognition motifs that selectively bind a ligand. In fact, the part that is not visible in the model (residues 535–570)—probably due to its flexibility and lack of secondary structure (as shown by the spectroscopic findings observed with the isolated region)—could become ordered and more rigid upon binding to a protein or nucleic acid. Since the top entrance of the tunnel and the helices from the insertions are located on opposite sides of the propeller, it is possible that the domain recruits two different binding partners at the same time (for a summary of the putative binding sites see Fig 9). It is also worth to note that C-D loop in blade 6 noticeably projects out of the bottom plane of the propeller in order to penetrate into a cavity of a symmetry-related molecule providing additional segments capable of interacting with other proteins. Moreover, if we take into consideration that Erb1 carries Nop7 and Ytm1 binding motifs towards its N-terminus it is plausible that the full length protein can establish multiple interactions within pre-ribosomal particles acting as a scaffold that plays an essential role in 60S maturation.


The carboxy-terminal domain of Erb1 is a seven-bladed ß-propeller that binds RNA.

Wegrecki M, Marcin W, Neira JL, Bravo J - PLoS ONE (2015)

Summary of the areas of Erb1Ct that are more likely to mediate protein-protein or protein-RNA interactions.The region corresponding to the conserved hot-spot residues is shown in green, the positively charged stretch of amino acids that might interact with RNA is highlighted in magenta, navy blue and red areas correspond to the conserved parts of the domain that establish important crystal contacts with symmetrically related molecules.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400149&req=5

pone.0123463.g009: Summary of the areas of Erb1Ct that are more likely to mediate protein-protein or protein-RNA interactions.The region corresponding to the conserved hot-spot residues is shown in green, the positively charged stretch of amino acids that might interact with RNA is highlighted in magenta, navy blue and red areas correspond to the conserved parts of the domain that establish important crystal contacts with symmetrically related molecules.
Mentions: Recently, it has been postulated that the WD40 proteins can also establish interactions by additional extensions or insertions that can occur between blades of the propeller [47]. It could be valid for Erb1 because, as we show here, it contains a long region that is introduced into WD2 and forms two visible α-helices and an additional strand. Residues in the propeller, outside the insertion, can contribute to the folding of the observed secondary motifs in this area. While the extra strand in blade 2 is probably necessary for structural stability of the inserted region and the propeller, the helices form an important protrusion that could serve as recognition motifs that selectively bind a ligand. In fact, the part that is not visible in the model (residues 535–570)—probably due to its flexibility and lack of secondary structure (as shown by the spectroscopic findings observed with the isolated region)—could become ordered and more rigid upon binding to a protein or nucleic acid. Since the top entrance of the tunnel and the helices from the insertions are located on opposite sides of the propeller, it is possible that the domain recruits two different binding partners at the same time (for a summary of the putative binding sites see Fig 9). It is also worth to note that C-D loop in blade 6 noticeably projects out of the bottom plane of the propeller in order to penetrate into a cavity of a symmetry-related molecule providing additional segments capable of interacting with other proteins. Moreover, if we take into consideration that Erb1 carries Nop7 and Ytm1 binding motifs towards its N-terminus it is plausible that the full length protein can establish multiple interactions within pre-ribosomal particles acting as a scaffold that plays an essential role in 60S maturation.

Bottom Line: This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat.The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding.Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, c/ Jaime Roig 11, 46010 Valencia, Spain.

ABSTRACT
Erb1 (Eukaryotic Ribosome Biogenesis 1) protein is essential for the maturation of the ribosomal 60S subunit. Functional studies in yeast and mammalian cells showed that altogether with Nop7 and Ytm1 it forms a stable subcomplex called PeBoW that is crucial for a correct rRNA processing. The exact function of the protein within the process remains unknown. The N-terminal region of the protein includes a well conserved region shown to be involved in PeBoW complex formation whereas the carboxy-terminal half was predicted to contain seven WD40 repeats. This first structural report on Erb1 from yeast describes the architecture of a seven-bladed β-propeller domain that revealed a characteristic extra motif formed by two α-helices and a β-strand that insert within the second WD repeat. We performed analysis of molecular surface and crystal packing, together with multiple sequence alignment and comparison of the structure with other β-propellers, in order to identify areas that are more likely to mediate protein-protein interactions. The abundance of many positively charged residues on the surface of the domain led us to investigate whether the propeller of Erb1 might be involved in RNA binding. Three independent assays confirmed that the protein interacted in vitro with polyuridilic acid (polyU), thus suggesting a possible role of the domain in rRNA rearrangement during ribosome biogenesis.

No MeSH data available.


Related in: MedlinePlus