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Molecular basis for N-terminal acetylation by the heterodimeric NatA complex

Abstract

N-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this cotranslational modification, the heterodimeric NatA complex has the most diversity for substrate selection and modifies the majority of all N-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100-kDa holo-NatA complex from Schizosaccharomyces pombe, in the absence and presence of a bisubstrate peptide-CoA–conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 tetratricopeptide motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.

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Figure 1: Overall structure of the NatA complex bound to acetyl CoA.
Figure 2: Structure of the Naa10p monomer bound to acetyl CoA.
Figure 3: Inhibitor structures and IC50 curves.
Figure 4: Structure of the NatA complex bound to a bisubstrate inhibitor.
Figure 5: The active site of the NatA complex.

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Acknowledgements

This work was supported by US National Institutes of Health (NIH) grant GM060293 (R.M.) and NIH training grant GM071339 (G.L.). We acknowledge the use of the Wistar Proteomics Core facility for the work reported here, which is supported in part by NIH grant CA010815. T.A. was supported by the Research Council of Norway and the Norwegian Cancer Society. We also acknowledge Marmorstein laboratory members and E. Skordalakes for helpful discussions.

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Contributions

G.L. performed all of the structural and biochemical experiments described in the manuscript, and J.M.G. carried out inhibitor synthesis. G.L. prepared manuscript figures, text and videos; H.F. carried out preliminary inhibition studies that led to experiments reported in the manuscript; R.M. designed and supervised experiments by G.L. and prepared manuscript text. T.A. supervised the experiments of H.F. and prepared manuscript text. E.J.P. supervised the experiments of J.M.G. All authors read and approved the submitted manuscript.

Corresponding author

Correspondence to Ronen Marmorstein.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 (PDF 12310 kb)

An overall view of the NatA complex structure

The view shown in Fig. 1A is shown rotating 360° on the y-axis followed by 360° on the x-axis. (AVI 17786 kb)

Global conformational shifts in Naa10p upon Naa15p binding

This video begins with the uncomplexed Naa10p and highlights all residues featured in Figures 1c,d. It first shows the position of these residues in the uncomplexed Naa10p and a morph shows the change in position of these residues upon Naa15p binding. (AVI 29209 kb)

Naa10p active site conformational changes upon Naa15p binding

This movie shows a morph that highlights the change in position of Naa10p residues Leu22, Glu24, Tyr26, Arg113 and Tyr139 upon Naa15p binding. The morph is shown twice, once with AcCoA bound to Naa10p and again with the bisubstrate inhibitor-bound Naa10p. (AVI 12648 kb)

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Liszczak, G., Goldberg, J., Foyn, H. et al. Molecular basis for N-terminal acetylation by the heterodimeric NatA complex. Nat Struct Mol Biol 20, 1098–1105 (2013). https://doi.org/10.1038/nsmb.2636

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