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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.


A canonical Asp/His/Ser triad necessary for correct blade organization.Conserved residues participating in the crucial hydrogen bond formation are shown and labelled. The distances between the atoms directly involved in H-H bonding are also represented.
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pone.0123463.g002: A canonical Asp/His/Ser triad necessary for correct blade organization.Conserved residues participating in the crucial hydrogen bond formation are shown and labelled. The distances between the atoms directly involved in H-H bonding are also represented.

Mentions: The solved structure of the C-terminal domain of Erb1 has confirmed that it folds into a seven-bladed β-propeller as previously predicted [1]. The blade organization and the nomenclature are shown on the Fig 1b and 1c. Structure analysis led us to slightly extend exact boundaries of the domain (residues 427–807) towards the N-term, when compared to the sequence-based prediction (residues 435–807) because the strand D (outermost) of blade 7 (most C-terminal) is actually formed by residues 427–433 which participate in the “velcro-like” closure of the domain (Fig 1b). Curiously, none of the WD repeats contains the eponymous WD motif but they rather present HD/YD dipeptides at the end of the strand C. Similarly to other WD40 domains, no clear pattern can be observed between the sequences of the repeats, although the hydrophobic core of the domain is well conserved and forms intra-molecular interactions necessary for proper folding. One of the most conserved features common for the β-propeller folds is the presence of a non-variable Asp in the loops that connect strands B and C of each blade. This residue is involved in stabilization of the domain as it forms a triad with a conserved His from the GH motif and a Ser/Thr residue placed in strand B. In Erb1, five of B-C loops contain an Asp residue but only four of them are truly conserved (red boxes Fig 1c) and the triad appears only in blades 1, 6 and 7 (Fig 2 and red squares in the alignment from Fig 1c). In loop 2B-2C there is a glutamic acid (Glu508) and in loop 4B-4C a glutamine (Gln659), both are conserved and establish a network of interactions that stabilizes the folding but is not similar to the canonical Asp-His-Ser/Thr triad. In the third blade, non-conserved Asp615 seems to be important for inter-blade interactions as it establishes hydrogen bonds with neighboring residues (Lys595 and Ile641), but it is rather to be substituted by a Gln in higher eukaryotes (Gln556 in human Bop1). It has been proposed that the conservation of the Asp residue could be correlated with the interacting His which means that if a WD repeat lacks the Asp it would also loose the His during evolution [31]. This seems to be true for Erb1 as the His from D-A loop is only conserved in the three repeats that form the triad with Asp. At last, Asp701 from B-C loop of blade 5 is fully conserved but the His is not present, thus the triad cannot be formed. Instead, this residue altogether with conserved Arg703 makes electrostatic and hydrogen-bonds that stabilize the fifth blade.


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)

A canonical Asp/His/Ser triad necessary for correct blade organization.Conserved residues participating in the crucial hydrogen bond formation are shown and labelled. The distances between the atoms directly involved in H-H bonding are also represented.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123463.g002: A canonical Asp/His/Ser triad necessary for correct blade organization.Conserved residues participating in the crucial hydrogen bond formation are shown and labelled. The distances between the atoms directly involved in H-H bonding are also represented.
Mentions: The solved structure of the C-terminal domain of Erb1 has confirmed that it folds into a seven-bladed β-propeller as previously predicted [1]. The blade organization and the nomenclature are shown on the Fig 1b and 1c. Structure analysis led us to slightly extend exact boundaries of the domain (residues 427–807) towards the N-term, when compared to the sequence-based prediction (residues 435–807) because the strand D (outermost) of blade 7 (most C-terminal) is actually formed by residues 427–433 which participate in the “velcro-like” closure of the domain (Fig 1b). Curiously, none of the WD repeats contains the eponymous WD motif but they rather present HD/YD dipeptides at the end of the strand C. Similarly to other WD40 domains, no clear pattern can be observed between the sequences of the repeats, although the hydrophobic core of the domain is well conserved and forms intra-molecular interactions necessary for proper folding. One of the most conserved features common for the β-propeller folds is the presence of a non-variable Asp in the loops that connect strands B and C of each blade. This residue is involved in stabilization of the domain as it forms a triad with a conserved His from the GH motif and a Ser/Thr residue placed in strand B. In Erb1, five of B-C loops contain an Asp residue but only four of them are truly conserved (red boxes Fig 1c) and the triad appears only in blades 1, 6 and 7 (Fig 2 and red squares in the alignment from Fig 1c). In loop 2B-2C there is a glutamic acid (Glu508) and in loop 4B-4C a glutamine (Gln659), both are conserved and establish a network of interactions that stabilizes the folding but is not similar to the canonical Asp-His-Ser/Thr triad. In the third blade, non-conserved Asp615 seems to be important for inter-blade interactions as it establishes hydrogen bonds with neighboring residues (Lys595 and Ile641), but it is rather to be substituted by a Gln in higher eukaryotes (Gln556 in human Bop1). It has been proposed that the conservation of the Asp residue could be correlated with the interacting His which means that if a WD repeat lacks the Asp it would also loose the His during evolution [31]. This seems to be true for Erb1 as the His from D-A loop is only conserved in the three repeats that form the triad with Asp. At last, Asp701 from B-C loop of blade 5 is fully conserved but the His is not present, thus the triad cannot be formed. Instead, this residue altogether with conserved Arg703 makes electrostatic and hydrogen-bonds that stabilize the fifth blade.

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.