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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.


Analysis of crystal packing.(a) Overview of crystal contacts of Erb1 monomer (blue) with symmetry related molecules (grey) shows that the top and bottom areas of the propeller are not involved in crystallographic interactions. (b) Helix H2 interacts with symmetrically related molecule (shown in pink). (c) 6C-7D loop penetrates deeply into a conserved cavity of another monomer (in pink). The residues directly involved in crystal packing are labelled in (b) and (c).
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pone.0123463.g003: Analysis of crystal packing.(a) Overview of crystal contacts of Erb1 monomer (blue) with symmetry related molecules (grey) shows that the top and bottom areas of the propeller are not involved in crystallographic interactions. (b) Helix H2 interacts with symmetrically related molecule (shown in pink). (c) 6C-7D loop penetrates deeply into a conserved cavity of another monomer (in pink). The residues directly involved in crystal packing are labelled in (b) and (c).

Mentions: From a crystallographic point of view, unlike in several crystal structures of β-propellers [33–35], the extensive top or bottom areas of the domain do not form many contacts with symmetry-related molecules but the interactions are rather maintained laterally through the outermost loops and strands (Fig 3a). Manual inspection of the unit cell and analysis by Pisa Server [36] showed that a single monomer contacted six other molecules making three small interfaces involved in crystal packing. Two of them arose in the bottom part of the propeller where the alpha-helix H2 orientates in proximity of blades 1 and 7 from one symmetry related monomer and the loops 5B-5C and 6D-6A from another propeller (Fig 3b). The third area corresponds to the long 6C-7D loop which forms an important extension and introduces Asp757, Met758 and Met759 into a cavity formed between Phe635, Tyr665 and Gln670 from blades 3 and 4 (Fig 3c). Both the loop and the cavity are well conserved within Erb1 family and may constitute additional elements involved in protein binding. The central axis of the propeller is filled with solvent (water) molecules.


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)

Analysis of crystal packing.(a) Overview of crystal contacts of Erb1 monomer (blue) with symmetry related molecules (grey) shows that the top and bottom areas of the propeller are not involved in crystallographic interactions. (b) Helix H2 interacts with symmetrically related molecule (shown in pink). (c) 6C-7D loop penetrates deeply into a conserved cavity of another monomer (in pink). The residues directly involved in crystal packing are labelled in (b) and (c).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123463.g003: Analysis of crystal packing.(a) Overview of crystal contacts of Erb1 monomer (blue) with symmetry related molecules (grey) shows that the top and bottom areas of the propeller are not involved in crystallographic interactions. (b) Helix H2 interacts with symmetrically related molecule (shown in pink). (c) 6C-7D loop penetrates deeply into a conserved cavity of another monomer (in pink). The residues directly involved in crystal packing are labelled in (b) and (c).
Mentions: From a crystallographic point of view, unlike in several crystal structures of β-propellers [33–35], the extensive top or bottom areas of the domain do not form many contacts with symmetry-related molecules but the interactions are rather maintained laterally through the outermost loops and strands (Fig 3a). Manual inspection of the unit cell and analysis by Pisa Server [36] showed that a single monomer contacted six other molecules making three small interfaces involved in crystal packing. Two of them arose in the bottom part of the propeller where the alpha-helix H2 orientates in proximity of blades 1 and 7 from one symmetry related monomer and the loops 5B-5C and 6D-6A from another propeller (Fig 3b). The third area corresponds to the long 6C-7D loop which forms an important extension and introduces Asp757, Met758 and Met759 into a cavity formed between Phe635, Tyr665 and Gln670 from blades 3 and 4 (Fig 3c). Both the loop and the cavity are well conserved within Erb1 family and may constitute additional elements involved in protein binding. The central axis of the propeller is filled with solvent (water) molecules.

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.