Histone deacetylase 6 enzyme (HDAC6)

 

Histone deacetylase 6 enzyme (HDAC6) is a metalloenzyme, part of the HDAC family. The HDAC family includes 18 isoforms which are grouped into four classes (I, II, III, and IV). HDACs in class III use an NAD+ cofactor, whilst the others are metalloenzymes which use a Zn(II) metal ion centre. HDAC6 is in class II and is involved in the maintenance of a cell's shape and its polarity during cell division and migration, intracellular transport and angiogenesis.

HDACs catalyse the removal of the acyl group from a lysine amino acid of the substrate of nuclear and cytosol proteins. In general, protein acylation and deacylation processes are a key part of cell cycle regulation.

HDAC6 has a heterodimeric structure with two different catalytic domains, CD1 and CD2. The domains present a similar structure but show differing substrate specificities and their roles remain unclear. HDAC6 is of interest for its role in the fight against cancer and various other pathologies.

 

Reference Protein and Structure

Sequence
F8W4B7 UniProt (3.5.1.98) IPR000286 (Sequence Homologues) (PDB Homologues)
Biological species
Danio rerio (Zebrafish) Uniprot
PDB
5g0i - Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat A (1.99 Å) PDBe PDBsum 5g0i
Catalytic CATH Domains
3.40.800.20 CATHdb (see all for 5g0i)
Cofactors
Zinc(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.5.1.98)

water
CHEBI:15377ChEBI
+
N(6)-acetyl-L-lysine residue
CHEBI:61930ChEBI
→
acetate
CHEBI:30089ChEBI
+
L-lysinium residue
CHEBI:29969ChEBI
Alternative enzyme names: HDAC,

Enzyme Mechanism

Introduction

In this mechanism proposed for both the CD1 and CD2 domains of HDAC6, a hydrogen bond network activates a water molecule for nucleophilic attack on the amide carbon of the substrate, forming a tetrahedral intermediate. A proton from the protonated imidazole ring of His193 is transferred to the nitrogen of the substrate, forming acetic acid and eliminating the deacylated Lys product. Entry of a water molecule and substrate molecule into the active site regenerates the enzyme for another turnover. DFT-based computations show the rate-limiting step of the reaction is the nucleophilic attack of the catalytic water for peptide bond hydrolysis in both the CD1 and CD2 domains.

Catalytic Residues Roles

UniProt PDB* (5g0i)
Tyr363 Tyr363(341)A Tyr363 hydrogen bonds the substrate. hydrogen bond donor
His193 His193(171)A Involved in a hydrogen bonding network in the enzyme-substrate complex. hydrogen bond donor, proton donor
His192 His192(170)A His192 activates the water molecule for nucleophilic attack on the substrate. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asp228 Asp228(206)A Asp228 accepts a proton from His192 in the first step of the reaction. This enables His192 to activate the water molecule for nucleophilic attack. hydrogen bond donor, proton acceptor
His232, Asp323, Asp230 His232(210)A, Asp323(301)A, Asp230(208)A Asp230, His232 and Asp323 coordinate to the Zn(II) centre. metal ligand
*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

rate-determining step, aromatic bimolecular nucleophilic addition, intermediate formation, coordination to a metal ion, overall product formed, proton transfer, unimolecular elimination by the conjugate base

References

  1. Prejanò M et al. (2021), ACS Catal, 11, 3084-3093. Insights into the Catalytic Mechanism of Domains CD1 and CD2 in Histone Deacetylase 6 from Quantum Calculations. DOI:10.1021/acscatal.0c04729.
  2. Hai Y et al. (2016), Nat Chem Biol, 12, 741-747. Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. DOI:10.1038/nchembio.2134. PMID:27454933.

Step 1. A structured hydrogen bond network activates a water molecule for nucleophilic attack on amide carbon of the substrate. This forms a tetrahedral intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His193(171)A hydrogen bond donor
His192(170)A hydrogen bond donor
Tyr363(341)A hydrogen bond donor
His232(210)A metal ligand
Asp323(301)A metal ligand
Asp230(208)A metal ligand
Asp228(206)A proton acceptor
His192(170)A proton acceptor, proton donor

Chemical Components

rate-determining step, ingold: aromatic bimolecular nucleophilic addition, intermediate formation, coordination to a metal ion

Step 2. A proton from the protonated imidazole ring of His193 is transferred to the nitrogen of the substrate. This induces C-N bond cleavage and forms the deacylated Lys and acetic acid products.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His232(210)A metal ligand
Asp323(301)A metal ligand
Asp230(208)A metal ligand
Asp228(206)A hydrogen bond donor
His192(170)A hydrogen bond acceptor
His193(171)A proton donor

Chemical Components

overall product formed, proton transfer, ingold: unimolecular elimination by the conjugate base
Download: Image, Marvin File

Step 1. A structured hydrogen bond network activates a water molecule for nucleophilic attack on amide carbon of the substrate. This forms a tetrahedral intermediate.

Step 2. A proton from the protonated imidazole ring of His193 is transferred to the nitrogen of the substrate. This induces C-N bond cleavage and forms the deacylated Lys and acetic acid products.

Products.

Contributors

Noa Marson, Antonio Ribeiro