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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

Top face of the β-propeller contains “hot spot” residues.(a) Top face of the propeller showing the position (in red) of the residues most likely to participate in macromolecular interactions as predicted by WDSP server (http://wu.scbb.pkusz.edu.cn/wdsp/). (b) Superposition of Lis1 (pink, PDB: 1VYH) with Erb1 β-propeller. The side chains of the conserved amino acids are shown and labeled.
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pone.0123463.g006: Top face of the β-propeller contains “hot spot” residues.(a) Top face of the propeller showing the position (in red) of the residues most likely to participate in macromolecular interactions as predicted by WDSP server (http://wu.scbb.pkusz.edu.cn/wdsp/). (b) Superposition of Lis1 (pink, PDB: 1VYH) with Erb1 β-propeller. The side chains of the conserved amino acids are shown and labeled.

Mentions: In addition, it has been proposed that the central channel of WD domains could work as a scaffold that adapts for recognition of different ligands through side-chains of three residues from each blade: the one right before the strand A (A-1), the one just after strand B (B+1) and the second residue in the strand A (A2), thus making this portion of the propeller an universal but variable binding motif. When we inspected these positions in Erb1Ct a strong conservation, especially in blades 1, 5, 6 and 7, was observed. Our findings were confirmed by WDSP web server which predicted hot-spot residues on the surface that were likely to be responsible for high-affinity interactions with other proteins [40] (Fig 6a). Moreover, those conserved positions seem to be related to Erb1/Bop1 function because they vary when compared to seven-bladed propellers from other families. Nevertheless, three of these superficial conserved amino acids, Asp457, Arg727 and Asp743 are also invariable in another family of WD repeat-containing proteins called Lis1 where they were shown to be involved in recognition of other macromolecules [41] (Fig 6b).


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)

Top face of the β-propeller contains “hot spot” residues.(a) Top face of the propeller showing the position (in red) of the residues most likely to participate in macromolecular interactions as predicted by WDSP server (http://wu.scbb.pkusz.edu.cn/wdsp/). (b) Superposition of Lis1 (pink, PDB: 1VYH) with Erb1 β-propeller. The side chains of the conserved amino acids are shown and labeled.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123463.g006: Top face of the β-propeller contains “hot spot” residues.(a) Top face of the propeller showing the position (in red) of the residues most likely to participate in macromolecular interactions as predicted by WDSP server (http://wu.scbb.pkusz.edu.cn/wdsp/). (b) Superposition of Lis1 (pink, PDB: 1VYH) with Erb1 β-propeller. The side chains of the conserved amino acids are shown and labeled.
Mentions: In addition, it has been proposed that the central channel of WD domains could work as a scaffold that adapts for recognition of different ligands through side-chains of three residues from each blade: the one right before the strand A (A-1), the one just after strand B (B+1) and the second residue in the strand A (A2), thus making this portion of the propeller an universal but variable binding motif. When we inspected these positions in Erb1Ct a strong conservation, especially in blades 1, 5, 6 and 7, was observed. Our findings were confirmed by WDSP web server which predicted hot-spot residues on the surface that were likely to be responsible for high-affinity interactions with other proteins [40] (Fig 6a). Moreover, those conserved positions seem to be related to Erb1/Bop1 function because they vary when compared to seven-bladed propellers from other families. Nevertheless, three of these superficial conserved amino acids, Asp457, Arg727 and Asp743 are also invariable in another family of WD repeat-containing proteins called Lis1 where they were shown to be involved in recognition of other macromolecules [41] (Fig 6b).

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