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Structural Basis for Complex Formation of GCN5 Histone Acetyltransferase with H3 and Coenzyme A

 Harry Hurley '14 with Michael Gallaher '14


I. Introduction

The GCN5 Histone Acetyltransferase (HAT) is a histone-modifying protein found in Tetrahymena thermophilia.  Histone Acetyltransferases such as this one are crucial to successful transcription.  DNA in chromatin is bound about Histones, and HAT is the principal enzyme to signal Histone release.  It does this through acetylation; acetylated Histone tails have a higher affinity for FACT, which will cause the Histone to come apart, allowing RNA polymerase to transcribe the gene.

GCN5 targets the Carboxy-terminal end of the of the Histone.  A phosphorylated Ser10 on H3 has shown to raise the affinity of GCN5 binding.  GCN5 can transfer an acetyl group from a substrate,  , to the carboxy-terminal tail on H3. This increases the affinity for FACT binding and activity, ultimately allowing transcription to proceed along the gene previously bound by the histone.

II. General Structure

GCN5 is a monomer of roughly 22,000 molecular weight, composed of a 162 peptide long polypeptide chain. GCN5 is a globular protein made up of five α-helices and a six-stranded β-sheet. These   combine to form a globular domain with a pronounced L-shaped cleft.  The interaction surface for the H3 substrate is within the longer segment of the cleft, defined by GCN5 and the of CoA.

The GCN5 monomer forms a complex with acetyl CoA, which donates the acetyl group, and a 19 peptide carboxy terminal domain of the H3 histone subunit. The on the H3 chain is responsible for accepting the acetyl group. Entry C-Terminal to the active site is mediated by the

III. CoA Binding 

is a both the acetylator and the stabilizing factor for the H3 peptide.  Since it is so crucial to these aspects, GCN5 activity, it must bind before anything else does.   The CoA - Protein interactions in the tGCN5/CoA/histone H3 peptide ternary complex are made by the β4-turn-α3 of the GCN5 domain with the pyrophosphate group and pantetheine arm of CoA.  Additional interactions are provided by the α1 helix of the N-terminal protein segment, and the β4-strand and the α4-turn regions in the

IV. H3 Binding

H3 is by the α1-turn-α2 N-terminal segment, and the β5-turn-α4 C-terminal segment. A key factor to the binding of H3 is a phosphorylated Ser10 residue on H3.

 It promotes extensive interactions between Thr11 and the GCN5 residues at the base of the   The orientation of Thr11 is dependent on phospho-Ser10 residue.  The Thr11 side chain from H3 is buried deeply in the base of the cleft, making substantial van der Waals interactions with the of Arg113, Tyr115, and Glu122. Thr11 also forms a hydrogen bond with Glu122. Here is the full H3 polypeptide, not included in the PDB.


V. Acetylation

Acetylation of the Lys14 residue hinges upon the proper K14-G15-L16-G17 to bind to the GCN5 active site properly.  The highly reactive Lys14 residue of the histone H3 peptide is directly anchored to the substrate binding site by van der Waals interactions with Val 123 and Leu 126 in the β4 sheet at the base of the peptide cleft and by the CoA cofactor, and by hydrogen bonds to the backbone carbonyl group of Ala124,and the of CoA. The region of the β4 strand that interacts with the Lys14 residue of the histone H3 peptide has a which appears to be essential to facilitate these protein-substrate interactions as well as to point the backbone carbonyls of residues Val 123 and Ala124 into the histone-binding cleft to facilitate an electrostatic attraction for the lysine substrate.

VI. Implications

One novel observation of this structure is that the phosphorylated histone H3 undergoes a significant structural rearrangement when compared to the nonphosphorylated histone (Clements et al., 2003).  The result is a change in the overall architecture of the ternary GCN5 complex, promoting more interactions between GCN5 and the histone H3 substrate (Clements et al., 2003).  In particular, the interaction surface for the peptide N-terminus has moved significantly from the GCN5 α2 helix with the unmodified H3 peptide to the α5-β6 loop in the case of the phosphorylated H3 peptide (Clements et al., 2003).  No parallel has been found among comparable histone acetyltransferases of this phosphorylated region.  Phospho-Ser10 enhancement of HAT activity is GCN5 specific, rather than generally applicable to all histone acetyltransferases (Rojas et al., 1999).

VII. References

Clements, A., Poux, A., Lo, W., Pillus, L., Berger, S., Marmorstein, R. August 2003.  Structural Basis for Histone and Phosphohistone Binding by the GCN5 Histone Acetyltransferase.  Molecular Cell, Vol. 12, 461-473.

Poux, A., Cebrat, M., Kim, C., Cole, P., Marmorstein, R. October 2002.  Structure of the GCN5 histone cetyltransferase bound to a bisubstrate inhibitor. PNAS, Vol. 99 no. 22 14065-14070.

Poux, A., and Marmorstein, R.  September, 2003.  Molecular Basis for GCN5/PCAF Histone Acetyltransferase Selectivity for Histone and Nonhistone Substrates.  Biochemistry, Vol. 42, 14366-14374.

Rojas, J., Trievel, R., Zhou, J., Mo, Y., Li, X., Berger, S., Allis, D., Marmorstein, R.  September 1999.  Structure of Tetrahymena GCN5 Bound to Coenzyme A and a Histone H3 Peptide.  Nature, Vol 401, 93-98.

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