Histone acetyltransferase (MYST family)

 

ESA1 Histone acyl transferase is able to catalyse the acylation of histone proteins at specific lysine residues, using acetyl coA as the acyl donor for the reaction. Acylation of histone proteins is important in the regulatation of DNA transcription, as it causes the chromasones to condense and become inaccessible to the enzymes required for unwinding and unzipping the DNA. As a result study of the mechanism by which acylation occurs is of interest to geneticists, and opens the possibility of manipulation of gene expression by designing activators or inhibitors of the enzymes catalysing the process.

Histone acyl transferases in eukaryotes show much sequence homology, and can consequently be assigned to a superfamily (HAT). However, the mechanism of reaction has been previously thought to be not the same where the MYST subfamily, of which ESA1 is a representative, have an acylated enzyme intermediate in the reaction mechanism. Despite this, it has been proposed more recently ESA1 when in complex with two accessory proteins does in fact work proceed with direct attack from the target lysine residue on the acetyl-COA. It has been suggested the catalytic mechanism may reflect the enzyme's physiological surroundings.

 

Reference Protein and Structure

Sequence
Q08649 UniProt (2.3.1.48) IPR002717 (Sequence Homologues) (PDB Homologues)
Biological species
Saccharomyces cerevisiae S288c (Baker's yeast) Uniprot
PDB
1mj9 - Crystal structure of yeast Esa1(C304S) mutant complexed with Coenzyme A (2.5 Å) PDBe PDBsum 1mj9
Catalytic CATH Domains
3.40.630.30 CATHdb (see all for 1mj9)
Click To Show Structure

Enzyme Reaction (EC:2.3.1.48)

L-lysinium residue
CHEBI:29969ChEBI
+
acetyl-CoA(4-)
CHEBI:57288ChEBI
→
N(6)-acetyl-L-lysine residue
CHEBI:61930ChEBI
+
coenzyme A(4-)
CHEBI:57287ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Histone acetokinase, Histone acetylase, Histone transacetylase, Nucleosome-histone acetyltransferase, Lysine acetyltransferase, Protein lysine acetyltransferase, Acetyl-CoA:histone acetyltransferase,

Enzyme Mechanism

Introduction

One reaction mechanism proposes it obeys ping-pong kinetics, with initial nucleophilic attack from Cys 304 on the acetyl-coA assisted by deprotonation of Cys 304 by the general base Glu 338. This results in the transfer of the acyl moiety to Cys 304. Histone binds and the target lysine is deprotonated by Glu 338 and then acts as a nucleophile, attacking the acyl moiety and resulting in Cys 304 acting as a leaving group. This transfers the acyl moiety to the Lysines epsilon NH group and forms the final product.

Catalytic Residues Roles

UniProt PDB* (1mj9)
Cys304 Ser304(147)A Acts as nucleophile to covalently attach to the acyl group of acetyl coA. Then acts as leaving group to allow transfer of the acyl group to the target lysine residue. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor
Glu338 Glu338(181)A Acts as general acid base first in the deprotonation of Cys 304 to allow it to act as a nucleophile, then in the deprotonation of the target lysine to allow it to act as a nucleophile. activator, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic substitution, enzyme-substrate complex formation, overall reactant used, intermediate formation, overall product formed, enzyme-substrate complex cleavage, intermediate terminated, inferred reaction step, native state of enzyme regenerated

References

  1. Yan Y et al. (2002), Nat Struct Biol, 9, 862-869. The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. DOI:10.1038/nsb849. PMID:12368900.
  2. Cortopassi WA et al. (2016), J Mol Graph Model, 67, 69-84. Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment. DOI:10.1016/j.jmgm.2016.04.011. PMID:27258188.
  3. Marmorstein R et al. (2014), Cold Spring Harb Perspect Biol, 6, a018762-. Writers and readers of histone acetylation: structure, mechanism, and inhibition. DOI:10.1101/cshperspect.a018762. PMID:24984779.

Step 1. Glu338 acts as a general base and deprotonates Cys304.

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Catalytic Residues Roles

Residue Roles
Ser304(147)A proton donor
Glu338(181)A proton acceptor

Chemical Components

proton transfer

Step 2. Deprotonated Cys304 performs nucleophilic attack on the terminal acetyl group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser304(147)A nucleophile

Chemical Components

ingold: bimolecular nucleophilic substitution, enzyme-substrate complex formation, overall reactant used, intermediate formation

Step 3. Proton transfer from Glu338 to CoA, which then leaves the active site.

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Catalytic Residues Roles

Residue Roles
Ser304(147)A covalently attached
Glu338(181)A proton donor

Chemical Components

proton transfer, overall product formed

Step 4. Histone binds. Glu338 acts as a general base to deprotonate the histone lysine.

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Catalytic Residues Roles

Residue Roles
Glu338(181)A activator
Ser304(147)A covalently attached
Glu338(181)A proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 5. Histone lysine acts as a nucleophile to attack the enzyme-substrate intermediate, acetylating itself.

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Catalytic Residues Roles

Residue Roles
Ser304(147)A proton acceptor, nucleofuge

Chemical Components

ingold: bimolecular nucleophilic substitution, enzyme-substrate complex cleavage, intermediate terminated, overall product formed, inferred reaction step

Step 6. Water restores active site catalytic residues.

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Catalytic Residues Roles

Residue Roles
Glu338(181)A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu338 acts as a general base and deprotonates Cys304.

Step 2. Deprotonated Cys304 performs nucleophilic attack on the terminal acetyl group.

Step 3. Proton transfer from Glu338 to CoA, which then leaves the active site.

Step 4. Histone binds. Glu338 acts as a general base to deprotonate the histone lysine.

Step 5. Histone lysine acts as a nucleophile to attack the enzyme-substrate intermediate, acetylating itself.

Step 6. Water restores active site catalytic residues.

Products.

Introduction

More recent mutagenesis studies have ruled out Cys304 as a catalytic residue in the Esa1 that physiologically associates to two accessory proteins to form the complex piccolo NuA4. Therefore, this mechanism proposal is different to the one seen in the other proposed mechanism. Esa1 is proposed to share a similar mechanism to Gcn5 histone acetyl transferase. Glu338 acts as a base catalyst to deprotonate the histone lysine's amine group. This promotes the direct nucleophilic attack of the lysine on the acetyl group on Acetyl-CoA to form a tetrahedral intermediate. This intermediate collapses to give the products of acetylated lysine and CoA.

Catalytic Residues Roles

UniProt PDB* (1mj9)
Glu338 Glu338(181)A Acts as a general base to promote the histone lysine nucleophilic attack on Acetyl-CoA. activator, proton acceptor, proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, overall reactant used, bimolecular nucleophilic addition, intermediate formation, unimolecular elimination by the conjugate base, intermediate terminated, overall product formed, native state of enzyme regenerated, inferred reaction step

References

  1. Berndsen CE et al. (2007), Biochemistry, 46, 623-629. Catalytic mechanism of a MYST family histone acetyltransferase. DOI:10.1021/bi602513x. PMID:17223684.
  2. Cortopassi WA et al. (2016), J Mol Graph Model, 67, 69-84. Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment. DOI:10.1016/j.jmgm.2016.04.011. PMID:27258188.
  3. Marmorstein R et al. (2014), Cold Spring Harb Perspect Biol, 6, a018762-. Writers and readers of histone acetylation: structure, mechanism, and inhibition. DOI:10.1101/cshperspect.a018762. PMID:24984779.

Step 1. Glu338 deprotonates histone lysine amine group, promoting its nucleophilicity.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu338(181)A activator, proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 2. Lysine performs a nucleophilic attack on the acetyl group on acetyl-CoA.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 3. Tetrahedral intermediate collapses to form the products CoA and acetylated lysine on the histone protein.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate terminated, overall product formed

Step 4. Glu338 is deprotonated to regenerate the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu338(181)A proton donor

Chemical Components

native state of enzyme regenerated, inferred reaction step, proton transfer
Download: Image, Marvin File

Step 1. Glu338 deprotonates histone lysine amine group, promoting its nucleophilicity.

Step 2. Lysine performs a nucleophilic attack on the acetyl group on acetyl-CoA.

Step 3. Tetrahedral intermediate collapses to form the products CoA and acetylated lysine on the histone protein.

Step 4. Glu338 is deprotonated to regenerate the active site.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Morwenna Hall