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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

Surface of Erb1 β-propeller is positively charged.Surface representation of the electrostatic potential of the domain (from red (-10) to blue (+10)kb T ec-1). The top face is shown on the left and the most positively charged area formed by blades 4 and 5 is visible on the right panel. The red oval indicates the position of Trp682.
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pone.0123463.g007: Surface of Erb1 β-propeller is positively charged.Surface representation of the electrostatic potential of the domain (from red (-10) to blue (+10)kb T ec-1). The top face is shown on the left and the most positively charged area formed by blades 4 and 5 is visible on the right panel. The red oval indicates the position of Trp682.

Mentions: Erb1 is known to bind rRNA as shown by UV-crosslinking experiments. It is possible that the β-propeller is involved in such a binding due to its highly positive charge (Fig 7). We used the PatchFinder Plus algorithm [42] to identify the biggest positive patch on the surface of the domain. Indeed, as seen for the electrostatic surface analysis, the tool found a big region of basic residues on the surface that included five blades and the entrance to the central channel on the top face of the propeller. Curiously, one of the few known structures of a WD domain bound to a nucleic acid is the one of DDB1-DDB2 complex with a DNA chain binding the protein through a cavity formed by the arginine and lysine residues oriented around the central tunnel of the propeller [43]. In Erb1 this area also contains well conserved basic amino acids: Arg441, Lys598 and Arg727.


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)

Surface of Erb1 β-propeller is positively charged.Surface representation of the electrostatic potential of the domain (from red (-10) to blue (+10)kb T ec-1). The top face is shown on the left and the most positively charged area formed by blades 4 and 5 is visible on the right panel. The red oval indicates the position of Trp682.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123463.g007: Surface of Erb1 β-propeller is positively charged.Surface representation of the electrostatic potential of the domain (from red (-10) to blue (+10)kb T ec-1). The top face is shown on the left and the most positively charged area formed by blades 4 and 5 is visible on the right panel. The red oval indicates the position of Trp682.
Mentions: Erb1 is known to bind rRNA as shown by UV-crosslinking experiments. It is possible that the β-propeller is involved in such a binding due to its highly positive charge (Fig 7). We used the PatchFinder Plus algorithm [42] to identify the biggest positive patch on the surface of the domain. Indeed, as seen for the electrostatic surface analysis, the tool found a big region of basic residues on the surface that included five blades and the entrance to the central channel on the top face of the propeller. Curiously, one of the few known structures of a WD domain bound to a nucleic acid is the one of DDB1-DDB2 complex with a DNA chain binding the protein through a cavity formed by the arginine and lysine residues oriented around the central tunnel of the propeller [43]. In Erb1 this area also contains well conserved basic amino acids: Arg441, Lys598 and Arg727.

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