User:Emily Leiderman/Sandbox 1

Introduction

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. 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 N-terminal domain stretches from residues 2-111 and the C-terminal domain extends from residues 122-320. Residues 112 – 121 are what are thought to construct the extended loop that connects the two domains.

Structure

Domains

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 Ile-217, Pro-257, Phe-261, in addition to further bonds resulting from residues 217-220 and 255-256. 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. 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

Several mechanisms for the transfer of the acetyl group to the Lys-12 of the histone have been proposed. One possible mechanism consists of a 2-step process. The acetyl group is first transferred to a holding intermediate on the enzyme before subsequently being transferred to Lys-12. There are two cysteine residues, Cys-107 and Cys-234, that could serve as sites to accept and acetyl group but are not in close enough proximity to the active site. Another proposed mechanism consists of an e-amino group on the Lys-12 that is modified so that it is nucleophilic enough to directly attack the carbonyl carbon to initiate the acetyl transfer. This mechanism requires that the Lys-12 residue possess a neutral charge. While this is atypical of lysine residues, one theory suggests that the environment of the catalytic site either stabilizes the uncharged state of lysine, or a proton is donated from Lys-12 of the histone to another residue in the protein during substrate binding. The structure The transfer mechanism is contingent on a conformational change and the formation of a functional gate that spans the concave groove over the bound Acetyl CoA.

Protein Gate

Active Residues

Homology to Other Proteins

References

Student Contributors