User:Emily Leiderman/Sandbox 1

Introduction

The reversible acetylation of lysine residues of histone has been proven to play an important role in the regulation of heterochromatin (inactive) and euchromatin (active). The role of the protein Histone Acetyltransferase is to transfer an acetyl group from to a lysine group found on a histone. This results in an increase in gene activity as the addition of acetyl groups to histones results in the formation of euchromatin. In this study we analyzed the structure and function of the HAT1 gene that’s derived from Saccharomyces cerevisiae. Analysis of the various binding sites and interaction mechanisms involved in the acetylation process in addition to the initial Acetyl CoA binding mechanism ^[1] .

Structure

The structure of HATs consist of a with at least 3 stranded antiparallel β-sheets and one α-helix spanning the length of the sheet. Specifically, Hat1 has an elongated and curved structure that is comprised of 320 residues. The elongated shape of Hat1 allows for the formation of a concave surface where Acetyl CoA binds to the protein.

Domains

It is composed of a mixture of helices and sheets that form two domains. The domains are connected via an extended loop region that together make up the quaternary structure of the protein. The stretches from residues 2-111 and the extends from residues 122-320. Residues 112–121 are what are thought to construct the extended loop that connects the two domains. Additionally, the C-terminal domain contains the active site.

Active Site

The concave groove mentioned above is where Acetyl CoA binds and is known to be the active site of the enzyme. The groove contains approximately 1100 Å of accessible surface area. Because Acetyl CoA exhibits a bent shape it is thought that the ligand is able to wrap itself around the protein upon binding. Functional studies state that a conformational change is likely after Acetyl CoA is bound; this conformational change results in the formation of a binding cleft for the target lysine residue to enter the backside of the active site to be Acetylated. The binding of the target histone does not result in any conformational change. The Lys-12 side chain is able to approach the carbonyl group from the backside of the active site adjacent to the gating region. Near 60% of the Acetyl CoA molecule is found buried in a highly non-polar region of the protein surface called the hydrophobic pocket.

Hydrophobic Pocket

The active site consists of the Acetyl CoA ligand bound to the enzyme in a groove on the surface of the protein. The ligand is held in place by several bonds to protein residues that result in the formation of a hydrophobic pocket. The hydrophobic pocket consists of the interacting side chains from residues , , , in addition to further bonds resulting from residues 217-220 and 255-256(9727486). The amide of main-chain Phe-220 hydrogen bonds to the carbonyl oxygen of the Acetyl group in the binding pocket. The main-chain amide of Asn-258 also donates a hydrogen bond from its side chain to oxygen PO5 of the pantothenic acid group(9727486). The binding within the hydrophobic pocket is further supplemented through the creation of a protein gate that establishes a bridge over the concave surface that serves to keep Acetyl CoA in place while the enzyme interacts with the histone.

Mechanism

Protein Gate

Homology to Other Proteins

References

Student Contributors