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Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide

Nature volume 401, pages 93–98 (1999)Cite this article

Abstract

Gene activation is a highly regulated process that requires the coordinated action of proteins to relieve chromatin repression and to promote transcriptional activation. Nuclear histone acetyltransferase (HAT) enzymes provide a mechanistic link between chromatin destabilization and gene activation by acetylating the ε-amino group of specific lysine residues within the amino-terminal tails of core histones to facilitate access to DNA by transcriptional activators1,2. Here we report the high-resolution crystal structure of the HAT domain of Tetrahymena GCN5 (tGCN5) bound with both its physiologically relevant ligands, coenzyme A (CoA) and a histone H3 peptide, and the structures of nascent tGCN5 and a tGCN5/acetyl-CoA complex. Our structural data reveal histone-binding specificity for a random-coil structure containing a G-K-X-P recognition sequence, and show that CoA is essential for reorienting the enzyme for histone binding. Catalysis appears to involve water-mediated proton extraction from the substrate lysine by a glutamic acid general base and a backbone amide that stabilizes the transition-state reaction intermediate. Comparison with related N-acetyltransferases indicates a conserved structural framework for CoA binding and catalysis, and structural variability in regions associated with substrate-specific binding.

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Figure 1: Overall structure of the ternary tGCN5/CoA/histone H3 peptide complex.
Figure 2: The tGCN5 binding site for the histone H3 peptide.
Figure 3: Comparison between tGCN5, tGCN5/acetyl-CoA and tGCN5/CoA/histone H3.
Figure 4: The tGCN5 active site.

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Acknowledgements

We thank J. Berendzen, B. Sweet and their staff for access to and help on beamline X8C at NSLS; D. Thiel and his staff for access to and help on beamlines A1 and F2 at CHESS; and R. Venkataramani, A. Clements, T. Stams and D. King for useful discussions. This work was supported by NIH grants to R.M., S.L.B. and C.D.A., an NIH Under-represented Minority Supplement to J.R.R., a Howard Hughes predoctoral fellowship to R.C.T. and a grant from the Fannie E. Rippel Foundation to R.M.

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Author notes

  1. C. David Allis

    Present address: Department of Biochemistry and Molecular Genetics, University of Virginia HSC, Charlottesville, Virginia, 22908, USA

Authors and Affiliations

  1. The Wistar Institute,

    Jeannie R. Rojas, Raymond C. Trievel, Yi Mo, Xinmin Li, Shelley L. Berger & Ronen Marmorstein

  2. Department of Chemistry,

    Jeannie R. Rojas, Yi Mo & Ronen Marmorstein

  3. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    Raymond C. Trievel, Xinmin Li & Ronen Marmorstein

  4. Department of Biology, University of Rochester, Rochester, 14627, New York, USA

    Jianxin Zhou & C. David Allis

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Correspondence to Ronen Marmorstein.

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Rojas, J., Trievel, R., Zhou, J. et al. Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide. Nature 401, 93–98 (1999). https://doi.org/10.1038/43487

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