Histone acetyltransferase (GCN5 family)

 

p300/CBP-associating factor (PCAF) from Homo sapiens is a histone acetyltransferase. It catalyses the transfer of an acetyl group from acetyl-coenzyme A to the epsilon-amino group of specific lysine residues within histone amino termini. The acetylation of histone plays a crucial role in the transcriptional activation of specific target genes, and in transcriptional regulation. Eukaryotic GCN5 acetyltransferases influence diverse biological processes by acetylating histones and non-histone proteins and regulating chromatin and gene-specific transcription as part of multiprotein complexes.

 

Reference Protein and Structure

Sequence
Q92830 UniProt (2.3.1.-, 2.3.1.48) IPR016376 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1z4r - Human GCN5 Acetyltransferase (1.74 Å) PDBe PDBsum 1z4r
Catalytic CATH Domains
3.40.630.30 CATHdb (see all for 1z4r)
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

The hydrophobic residues Phe 563, Phe 568, Ile 571, Val 572, Leu 606, Ile 637 and Tyr 640 raise the pKa of Glu 570, facilitating proton transfer. Glu 570 acts as a general base by abstracting a proton from the N atom of lysine of the substrate histone. This activates the N atom for nucleophilic attack on the C atom of the acetyl carbonyl on acetyl-CoA, forming a negatively charged, tetrahedral intermediate. This intermediate is stabilised by hydrogen bonding to the backbone amide of Cys 574. The carbonyl of the acetyl group is reformed, breaking the C-S bond to CoA, leaving the acetyl group covalently bound to the histone.

Catalytic Residues Roles

UniProt PDB* (1z4r)
Glu575 Glu575(81)A Glu 570 acts as a base by deprotonating the N atom of the lysine of the histone substrate. proton acceptor
Phe573, Val577, Ile576, Leu611, Ile642, Tyr645, Phe568 Phe573(79)A, Val577(83)A, Ile576(82)A, Leu611(117)A, Ile642(148)A, Tyr645(151)A, Phe568(74)A This hydrophobic residue serves to raise the pKa of Glu 570, facilitating proton transfer. electrostatic stabiliser
Cys579 (main-N) Cys579(85)A (main-N) The main chain amide of Cys 574 hydrogen bonds to the negatively charged tetrahedral intermediate, stabilising it. electrostatic stabiliser
*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, proton relay, rate-determining step, bimolecular nucleophilic addition, bimolecular elimination

References

  1. Clements A et al. (1999), EMBO J, 18, 3521-3532. Crystal structure of the histone acetyltransferase domain of the human PCAF transcriptional regulator bound to coenzyme A. DOI:10.1093/emboj/18.13.3521. PMID:10393169.
  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. Dutnall RN et al. (2002), Nat Struct Biol, 9, 888-891. Methyl magic and HAT tricks. DOI:10.1038/nsb1202-888. PMID:12447351.
  4. Trievel RC et al. (1999), Proc Natl Acad Sci U S A, 96, 8931-8936. Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator. DOI:10.1073/pnas.96.16.8931. PMID:10430873.

Step 1. Glu570 acts as a general base and abstracts a proton from the histone lysine via a water molecule.

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Catalytic Residues Roles

Residue Roles
Leu611(117)A electrostatic stabiliser
Ile642(148)A electrostatic stabiliser
Val577(83)A electrostatic stabiliser
Phe568(74)A electrostatic stabiliser
Tyr645(151)A electrostatic stabiliser
Phe573(79)A electrostatic stabiliser
Cys579(85)A (main-N) electrostatic stabiliser
Ile576(82)A electrostatic stabiliser
Glu575(81)A proton acceptor

Chemical Components

proton transfer, proton relay

Step 2. Nucleophilic attack by the histone lysine on the acetyl group of acetyl-CoA, forming a negatively charged, tetrahedral intermediate

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

rate-determining step, ingold: bimolecular nucleophilic addition

Step 3. The C-S bond to CoA breaks, leaving the acetyl group covalently bound to the histone. The protonation of the sulphur atom is inferred.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: bimolecular elimination
Download: Image, Marvin File

Step 1. Glu570 acts as a general base and abstracts a proton from the histone lysine via a water molecule.

Step 2. Nucleophilic attack by the histone lysine on the acetyl group of acetyl-CoA, forming a negatively charged, tetrahedral intermediate

Step 3. The C-S bond to CoA breaks, leaving the acetyl group covalently bound to the histone. The protonation of the sulphur atom is inferred.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, Craig Porter