User:Emily Leiderman/Sandbox 1
From Proteopedia
Histone Acetyltransferase 1
IntroductionAcetylation of lysine residues 5 and 12 found in histones are known to regulate the interconversion of chromatin structures between heterochromatin (inactive) and euchromatin (active) [1]. The role of Histone Acetyltransferase (HAT1) is to transfer an acetyl group from Acetyl-CoA to lysine 5 or lysine 12 on histone IV [2] . This results in an increase in gene activity via transcription activation. The addition of acetyl groups to histones results converts heterochromatin to its more euchromatin form [3]. As acetyl groups are added to lysine, the negatively charged histone begins to lose its negative charge allowing for the more relaxed and active chromatin structures to form. We analyzed the structure and function of the HAT1 gene that’s derived from Saccharomyces cerevisiae [4]. The particular protein model we investigated is called 1BOB and is found on the protein database. The various binding sites and interaction mechanisms involved in the acetylation process were analyzed in addition to the initial Acetyl CoA binding mechanism. StructureHistone Acetyltransferases consist of a comprised of a 3-stranded antiparallel β-sheet and one α-helix spanning the length of the sheet [1]. 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.
DomainsIt 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 [3]. 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 [3].
Active SiteThe concave groove mentioned above is where Acetyl CoA binds and is known to be the active site of the enzyme. he Acetyl-CoA binding site is nearly 1100 Å of surface area where several residues interact to simultaneously bind Acetyl CoA and the lysine target of acetylation [3]. 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 occurs after Acetyl CoA binds this conformational change and results in the formation of a for the target lysine residue to enter the backside of the active site to be acetylated [3]. The side chain of the Lysine to be acetylated enters the complex from the back side 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
Mechanism
Protein GateThe consists of several residues that coordinate a conformational change in the protein to hold the Acetyl CoA ligand in place. cooperate to create a bridge over Acetyl CoA [3]. The main chain amide of hydrogen bonds to the carbonyl oxygen of Asn-258 which allows for proper positioning of Asn-258 to bond with other residues and Acetyl CoA itself. The side chain amide of Asn-258 also binds via a water molecule (H2O-415) to Glu-162 on its main chain amide [3]. These bonds help secure the position of so that a hydrogen bond can be established from the side-chain amide to the PO5 carbonyl oxygen. Together, the side chains of Ile-161, Glu-162, and Asn-258 form a protein gate over the Acetyl CoA binding cleft. Hydrogen bonds further fixate Acetyl CoA by connecting the main chain amide of Glu-162 to the side chain amide of Asn-258. The side chain carbonyl oxygen of Phe-261 hydrogen bonds to its main chain amide to bridge the binding cleft over Acetyl-CoA. The gate allows for correct binding of Acetyl CoA. Once the ligand is bound, subsequent conformational changes of HAT1 take place allowing for Lys-12 to act as a nucleophile.
Medical RelevanceHistone acetyltransferases consists of 5 families: GNAT, MYST, p300/CBP, and Rtt109. HATs of these families have histone substrate specificity, such as lysine, and non-histone substrate specificity, such as proteins and transcription factors. Specifically, the acetylation of the particular residue, lysine 16 of histone H4, is crucial in maintaining a normal lamin A gene and genomic stability since a mutation in the lamin A gene can cause premature, rapid aging [7]. Hutchinson Gilford progeria, an example of an accelerated aging syndrome, is caused by a mutated lamin A producing the mutant protein progerin, resulting in the delayed response time of repair proteins during DNA damage [7]. A study done by Krishnan et. al showed that it was a defect in histone acetyltransferase, Mof, in Zmpste24-/- mice that allowed for the hypoacetylation of lysine 16 residue (H4K16) which lead to a delayed response in modified histones recruiting repair proteins to fix DNA damage. Thus, the inability of repair proteins to correct DNA damage suggests that cells get inclined to rapid aging and early senescence, resulting in syndromes such as Hutchinson Gilford progeria [7].
References
Student ContributorsKiran Kaur, Emily Leiderman, Benjamin Nick | ||||||||||||
