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The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.

Arnaudo N, Fernández IS, McLaughlin SH, Peak-Chew SY, Rhodes D, Martino F - Nat. Struct. Mol. Biol. (2013)

Bottom Line: The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown.The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis.

View Article: PubMed Central - PubMed

Affiliation: Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.

ABSTRACT
The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome. Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis.

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Sir3 N-terminal acetylation stabilizes the interaction of Sir3 BAH with the NCP(a) Superposition of the structures of the N-terminally acetylated (pink) and unacetylated (grey)10 BAH in complex with the NCP. (b) Detailed view of Ala2 (A2), N-ter-acetyl group (Nt-Ac), Loop3 and Helix8. (c) Detailed view of the interactions between the acetylated N-terminus of Sir3 and Loop3. (e) Close-up view of Sir3 Helix8–histone core interactions. (d) Detailed view of the acetylated Sir3 N-terminus.
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Figure 2: Sir3 N-terminal acetylation stabilizes the interaction of Sir3 BAH with the NCP(a) Superposition of the structures of the N-terminally acetylated (pink) and unacetylated (grey)10 BAH in complex with the NCP. (b) Detailed view of Ala2 (A2), N-ter-acetyl group (Nt-Ac), Loop3 and Helix8. (c) Detailed view of the interactions between the acetylated N-terminus of Sir3 and Loop3. (e) Close-up view of Sir3 Helix8–histone core interactions. (d) Detailed view of the acetylated Sir3 N-terminus.

Mentions: The structure of the N-terminal acetylated BAH in complex with the NCP was solved at 3.3Å resolution and it was superimposed to the structure of the unacetylated BAH bound to NCP (Fig. 2a,b). In addition to the multiple interactions involved in the recognition of the NCP by the BAH reported previously10, we observe a set of additional interactions arising from the acetylated N-terminus of Sir3 (Fig. 2c-e). As a result, loop3 and helix8 of Sir3 BAH are positioned closer to the histone core surface (Fig. 2b,c,e). In particular, the side chain of Asn80, located in loop3, is within hydrogen-bonding distance to the side chains of H2B Arg93 and H4 Glu74 (Fig. 2c and Supplementary Fig. 3b,c). Asn80 is part of a tight network of interactions where the position of H2B Arg93 side chain is stabilized by H4 His75, whereas H4 Glu74 side chain is hold in place by a potential hydrogen bond with H4 Arg67 (Fig. 2c and Supplementary Fig. 3d). Loop3 forms a pocket-like structure that holds H3 Lys79 in place like a key in a lock (Fig. 2c). The presence of several acidic amino acids in loop3 suggests that the side chain of H3 Lys79 can assume different orientations in the pocket, providing an explanation for the poor electron density observed for H3 Lys79. Well-defined experimental densities could be assigned to the other residues forming the pocket (Supplementary Fig. 3b-d).


The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.

Arnaudo N, Fernández IS, McLaughlin SH, Peak-Chew SY, Rhodes D, Martino F - Nat. Struct. Mol. Biol. (2013)

Sir3 N-terminal acetylation stabilizes the interaction of Sir3 BAH with the NCP(a) Superposition of the structures of the N-terminally acetylated (pink) and unacetylated (grey)10 BAH in complex with the NCP. (b) Detailed view of Ala2 (A2), N-ter-acetyl group (Nt-Ac), Loop3 and Helix8. (c) Detailed view of the interactions between the acetylated N-terminus of Sir3 and Loop3. (e) Close-up view of Sir3 Helix8–histone core interactions. (d) Detailed view of the acetylated Sir3 N-terminus.
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Related In: Results  -  Collection

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Figure 2: Sir3 N-terminal acetylation stabilizes the interaction of Sir3 BAH with the NCP(a) Superposition of the structures of the N-terminally acetylated (pink) and unacetylated (grey)10 BAH in complex with the NCP. (b) Detailed view of Ala2 (A2), N-ter-acetyl group (Nt-Ac), Loop3 and Helix8. (c) Detailed view of the interactions between the acetylated N-terminus of Sir3 and Loop3. (e) Close-up view of Sir3 Helix8–histone core interactions. (d) Detailed view of the acetylated Sir3 N-terminus.
Mentions: The structure of the N-terminal acetylated BAH in complex with the NCP was solved at 3.3Å resolution and it was superimposed to the structure of the unacetylated BAH bound to NCP (Fig. 2a,b). In addition to the multiple interactions involved in the recognition of the NCP by the BAH reported previously10, we observe a set of additional interactions arising from the acetylated N-terminus of Sir3 (Fig. 2c-e). As a result, loop3 and helix8 of Sir3 BAH are positioned closer to the histone core surface (Fig. 2b,c,e). In particular, the side chain of Asn80, located in loop3, is within hydrogen-bonding distance to the side chains of H2B Arg93 and H4 Glu74 (Fig. 2c and Supplementary Fig. 3b,c). Asn80 is part of a tight network of interactions where the position of H2B Arg93 side chain is stabilized by H4 His75, whereas H4 Glu74 side chain is hold in place by a potential hydrogen bond with H4 Arg67 (Fig. 2c and Supplementary Fig. 3d). Loop3 forms a pocket-like structure that holds H3 Lys79 in place like a key in a lock (Fig. 2c). The presence of several acidic amino acids in loop3 suggests that the side chain of H3 Lys79 can assume different orientations in the pocket, providing an explanation for the poor electron density observed for H3 Lys79. Well-defined experimental densities could be assigned to the other residues forming the pocket (Supplementary Fig. 3b-d).

Bottom Line: The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown.The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis.

View Article: PubMed Central - PubMed

Affiliation: Structural Studies Division, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.

ABSTRACT
The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome. Additionally, we present a new method for the production of protein-nucleosome complexes for structural analysis.

Show MeSH