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Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.

Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B - PLoS Pathog. (2011)

Bottom Line: We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10.Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism.We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

View Article: PubMed Central - PubMed

Affiliation: Centre National de la Recherche Scientifique and Université de la Méditerranée, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Marseille, France. etienne.decroly@afmb.univ-mrs.fr

ABSTRACT
Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2'-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

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Stick model of RNA bound to the nsp16 RNA binding groove and Sinefungin in the methyltransferase active site.A) In this representation, Sinefungin was preferred over SAH because one of its NH2 groups approximates the direction of a transferred CH3 group from the SAM substrate. Carbon is white, oxygen is red, nitrogen is blue and phosphorous is orange. Nsp16 and nsp10 are rendered as a solvent-accessible surface colored grey and wheat respectively. The Sinefungin molecule defines the methyltransferase active site. Missing residues in the 135-137 loop (see text) are indicated by a shaded blue dotted box. Position of Y30 and Y132 are indicated. Y30 generated poor electron density (see « Methods ») and its aromatic ring position has been manually adjusted before generation of this image. B) Close caption of the methyltransferase active site showing distance between the NH2 of Sinefungin to the 2′-O of the ribose of the first base, thus mimicking the position of the methyl of the S-adenosylmethionine.
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ppat-1002059-g005: Stick model of RNA bound to the nsp16 RNA binding groove and Sinefungin in the methyltransferase active site.A) In this representation, Sinefungin was preferred over SAH because one of its NH2 groups approximates the direction of a transferred CH3 group from the SAM substrate. Carbon is white, oxygen is red, nitrogen is blue and phosphorous is orange. Nsp16 and nsp10 are rendered as a solvent-accessible surface colored grey and wheat respectively. The Sinefungin molecule defines the methyltransferase active site. Missing residues in the 135-137 loop (see text) are indicated by a shaded blue dotted box. Position of Y30 and Y132 are indicated. Y30 generated poor electron density (see « Methods ») and its aromatic ring position has been manually adjusted before generation of this image. B) Close caption of the methyltransferase active site showing distance between the NH2 of Sinefungin to the 2′-O of the ribose of the first base, thus mimicking the position of the methyl of the S-adenosylmethionine.

Mentions: The nsp10/nsp16 complex absolutely requires an N7-methyl guanine capped RNA substrate to exhibit MTase activity[16]. The structural basis for the preferential binding to methylated N7-guanine versus non-methylated caps has been elucidated in four cases, those of VP39[27], eIF4E[43], CBC[44], and PB2[45] proteins (PDB codes 1AV6, 1EJ1, 1H2T, and 2VQZ, respectively) bound to cap analogues or capped RNAs. In these cases, the methylated base specificity is achieved through increased binding energy resulting from the stacking of the N7-methyl guanine between parallel aromatic residues of the cap binding protein. The presence of the methyl group greatly enhances π-π stacking, providing a dominant effect over unmethylated guanine[46]. Despite numerous attempts, cap analogues (m7GpppA, GpppA, m7GpppG, GpppG) and short capped RNA substrates (m7GpppA(C)n) could neither be co-crystallized with nsp10/nsp16 nor soaked and bound onto preformed nsp10/nsp16 crystals. However, the atomic coordinates of the N7-methyl guanine RNA oligomer in complex with VP39[47] provided data from which a model of RNA binding to the nsp16 protein was derived. SAM molecules identified in both structures were superimposed, and the VP39-bound RNA was positioned onto the nsp16 structure. After minimal manual adjustments not exceeding 5 Å, the VP39 RNA was a reasonably good fit into an nsp16 hydrophobic groove radiating from the catalytic site (Fig. 5), establishing very few contacts with nsp10. We note that the protein side diametrically opposite to the proposed hydrophobic RNA binding groove is highly positively charged (not shown), an observation that may account for the difficulty of achieving experimental RNA binding in the proposed RNA binding site. In the absence of robust data to guide docking of the guanine cap, the m7Gpp cap structure was not positioned in the structure but two possible N7-methylated cap guanine binding areas are indicated by arrows (Fig. 5). The first transcribed nucleotide together with its ribose receiving the methyl group fit well in the active site (Fig. 5, panel B) as predicted in the proposed mechanism. The same holds for the immediately preceding three nucleotides. The base of the first transcribed nucleotide may be held by contact with P134 and Y132, bending the extending RNA cap structure. Accordingly, the substitution of Y132 greatly depresses MTase activity (Table 2). We also note that Y132 is located in the vicinity of a highly mobile loop (residues 135-138) not always visible in our crystal structures suggesting that this loop may move in order to wrap the triphosphate moiety of the RNA cap and/or the RNA cap itself. The solvent exposed side chain of Y30 may also participate in RNA binding. In the model, the highly mobile side chain of Y30 was flipped out in an alternative conformation in order to open the groove. In that position, Y30 should specifically contact the third transcribed nucleotide. Our mutagenesis data confirms the importance of Y30 since its replacement with either Ala or Phe severely impairs MTase activity without affecting the interaction with nsp10 (Table 2).


Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.

Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert I, Gluais L, Papageorgiou N, Sharff A, Bricogne G, Ortiz-Lombardia M, Lescar J, Canard B - PLoS Pathog. (2011)

Stick model of RNA bound to the nsp16 RNA binding groove and Sinefungin in the methyltransferase active site.A) In this representation, Sinefungin was preferred over SAH because one of its NH2 groups approximates the direction of a transferred CH3 group from the SAM substrate. Carbon is white, oxygen is red, nitrogen is blue and phosphorous is orange. Nsp16 and nsp10 are rendered as a solvent-accessible surface colored grey and wheat respectively. The Sinefungin molecule defines the methyltransferase active site. Missing residues in the 135-137 loop (see text) are indicated by a shaded blue dotted box. Position of Y30 and Y132 are indicated. Y30 generated poor electron density (see « Methods ») and its aromatic ring position has been manually adjusted before generation of this image. B) Close caption of the methyltransferase active site showing distance between the NH2 of Sinefungin to the 2′-O of the ribose of the first base, thus mimicking the position of the methyl of the S-adenosylmethionine.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102710&req=5

ppat-1002059-g005: Stick model of RNA bound to the nsp16 RNA binding groove and Sinefungin in the methyltransferase active site.A) In this representation, Sinefungin was preferred over SAH because one of its NH2 groups approximates the direction of a transferred CH3 group from the SAM substrate. Carbon is white, oxygen is red, nitrogen is blue and phosphorous is orange. Nsp16 and nsp10 are rendered as a solvent-accessible surface colored grey and wheat respectively. The Sinefungin molecule defines the methyltransferase active site. Missing residues in the 135-137 loop (see text) are indicated by a shaded blue dotted box. Position of Y30 and Y132 are indicated. Y30 generated poor electron density (see « Methods ») and its aromatic ring position has been manually adjusted before generation of this image. B) Close caption of the methyltransferase active site showing distance between the NH2 of Sinefungin to the 2′-O of the ribose of the first base, thus mimicking the position of the methyl of the S-adenosylmethionine.
Mentions: The nsp10/nsp16 complex absolutely requires an N7-methyl guanine capped RNA substrate to exhibit MTase activity[16]. The structural basis for the preferential binding to methylated N7-guanine versus non-methylated caps has been elucidated in four cases, those of VP39[27], eIF4E[43], CBC[44], and PB2[45] proteins (PDB codes 1AV6, 1EJ1, 1H2T, and 2VQZ, respectively) bound to cap analogues or capped RNAs. In these cases, the methylated base specificity is achieved through increased binding energy resulting from the stacking of the N7-methyl guanine between parallel aromatic residues of the cap binding protein. The presence of the methyl group greatly enhances π-π stacking, providing a dominant effect over unmethylated guanine[46]. Despite numerous attempts, cap analogues (m7GpppA, GpppA, m7GpppG, GpppG) and short capped RNA substrates (m7GpppA(C)n) could neither be co-crystallized with nsp10/nsp16 nor soaked and bound onto preformed nsp10/nsp16 crystals. However, the atomic coordinates of the N7-methyl guanine RNA oligomer in complex with VP39[47] provided data from which a model of RNA binding to the nsp16 protein was derived. SAM molecules identified in both structures were superimposed, and the VP39-bound RNA was positioned onto the nsp16 structure. After minimal manual adjustments not exceeding 5 Å, the VP39 RNA was a reasonably good fit into an nsp16 hydrophobic groove radiating from the catalytic site (Fig. 5), establishing very few contacts with nsp10. We note that the protein side diametrically opposite to the proposed hydrophobic RNA binding groove is highly positively charged (not shown), an observation that may account for the difficulty of achieving experimental RNA binding in the proposed RNA binding site. In the absence of robust data to guide docking of the guanine cap, the m7Gpp cap structure was not positioned in the structure but two possible N7-methylated cap guanine binding areas are indicated by arrows (Fig. 5). The first transcribed nucleotide together with its ribose receiving the methyl group fit well in the active site (Fig. 5, panel B) as predicted in the proposed mechanism. The same holds for the immediately preceding three nucleotides. The base of the first transcribed nucleotide may be held by contact with P134 and Y132, bending the extending RNA cap structure. Accordingly, the substitution of Y132 greatly depresses MTase activity (Table 2). We also note that Y132 is located in the vicinity of a highly mobile loop (residues 135-138) not always visible in our crystal structures suggesting that this loop may move in order to wrap the triphosphate moiety of the RNA cap and/or the RNA cap itself. The solvent exposed side chain of Y30 may also participate in RNA binding. In the model, the highly mobile side chain of Y30 was flipped out in an alternative conformation in order to open the groove. In that position, Y30 should specifically contact the third transcribed nucleotide. Our mutagenesis data confirms the importance of Y30 since its replacement with either Ala or Phe severely impairs MTase activity without affecting the interaction with nsp10 (Table 2).

Bottom Line: We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10.Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism.We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

View Article: PubMed Central - PubMed

Affiliation: Centre National de la Recherche Scientifique and Université de la Méditerranée, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, Marseille, France. etienne.decroly@afmb.univ-mrs.fr

ABSTRACT
Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2'-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

Show MeSH
Related in: MedlinePlus