Palmitoyl[protein] hydrolase (type 2)

 

Palmitoyl protein thioesterase 2 (PPT2) is a lysosomal enzyme with thioesterase activity. It will remove palmitate from palmitoyl CoA but is unable to remove palmitate groups from several S-palmitoylated proteins; in this respect it differs from the closely related enzyme PPT1.

 

Reference Protein and Structure

Sequence
Q9UMR5 UniProt (3.1.2.-) IPR030295 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1pja - The crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent substrate specificities of the two lysosomal thioesterases (PPT1 and PPT2) (2.7 Å) PDBe PDBsum 1pja
Catalytic CATH Domains
3.40.50.1820 CATHdb (see all for 1pja)
Click To Show Structure

Enzyme Reaction (EC:3.1.2.22)

water
CHEBI:15377ChEBI
+
S-palmitoyl-L-cysteine residue
CHEBI:74151ChEBI
→
hexadecanoate
CHEBI:7896ChEBI
+
hydron
CHEBI:15378ChEBI
+
L-cysteine residue
CHEBI:29950ChEBI
Alternative enzyme names: Palmitoyl-(protein) hydrolase, Palmitoyl-protein thioesterase,

Enzyme Mechanism

Introduction

Like other alpha-beta hydrolases, PPT2 uses a Ser-His-Asp triad. Ser 111 acts as a nucleophile to attack the thioester carbonyl group, while His 283 deprotonates the attacking Ser 111 and Asp 228 functions to modify the pKa of His 283. The tetrahedral intermediate resulting from attack by Ser 111 is stabilised by an oxyanion hole composed of the backbone NH groups of Gln 112 and Leu 45. Collapse of the tetrahedral intermediate generates an acyl-enzyme intermediate, which is then hydrolysed by a water molecule that is deprotonated by His 283.

Catalytic Residues Roles

UniProt PDB* (1pja)
Ser111 Ser111A Acts as a nucleophile to attack the thioester carbonyl, forming an acyl-enzyme intermediate that is subsequently hydrolysed. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor
Leu45 (main-N), Gln112 (main-N) Leu45A (main-N), Gln112A (main-N) Backbone NH forms part of the oxyanion hole that stabilises the tetrahedral intermediate. electrostatic stabiliser
Asp228 Asp228A Modifies the pKa of His 283. increase basicity, electrostatic stabiliser
His283 His283A Deprotonates Ser 111. Protonates the departing thiol leaving group. Deprotonates the nucleophilic water molecule. 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

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

References

  1. Calero G et al. (2003), J Biol Chem, 278, 37957-37964. The Crystal Structure of Palmitoyl Protein Thioesterase-2 (PPT2) Reveals the Basis for Divergent Substrate Specificities of the Two Lysosomal Thioesterases, PPT1 and PPT2. DOI:10.1074/jbc.m301225200. PMID:12855696.

Step 1. His283 acts as a general base activating the Ser111 hydroxyl group for nucleophilic attack on the carbonyl carbon of the thio-ester bond. The third component of this catalytic triad- Asp228 acts to increase the basicity of the histidine. The oxyanion intermediate formed is stabilized by the amide groups of Gln112 and leu45.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser111A covalently attached
Asp228A electrostatic stabiliser
Gln112A (main-N) electrostatic stabiliser
Leu45A (main-N) electrostatic stabiliser
Asp228A increase basicity
His283A proton acceptor
Ser111A nucleophile, proton donor

Chemical Components

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

Step 2. The tetrahedral intermediate collapses and cysteine is eliminated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser111A covalently attached
Leu45A (main-N) electrostatic stabiliser
Gln112A (main-N) electrostatic stabiliser
Asp228A electrostatic stabiliser
His283A proton donor

Chemical Components

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

Step 3. His283 activates water for nucleophilic attack and another oxyanion intermediate is formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Leu45A (main-N) electrostatic stabiliser
Gln112A (main-N) electrostatic stabiliser
Asp228A electrostatic stabiliser, increase basicity
Ser111A covalently attached
His283A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition

Step 4. The tetrahedral intermediate collapses and Ser111 is eliminated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Leu45A (main-N) electrostatic stabiliser
Gln112A (main-N) electrostatic stabiliser
Asp228A electrostatic stabiliser
Ser111A nucleofuge, proton acceptor
His283A proton donor

Chemical Components

native state of enzyme regenerated, proton transfer, intermediate terminated, ingold: unimolecular elimination by the conjugate base, overall product formed
Download: Image, Marvin File

Step 1. His283 acts as a general base activating the Ser111 hydroxyl group for nucleophilic attack on the carbonyl carbon of the thio-ester bond. The third component of this catalytic triad- Asp228 acts to increase the basicity of the histidine. The oxyanion intermediate formed is stabilized by the amide groups of Gln112 and leu45.

Step 2. The tetrahedral intermediate collapses and cysteine is eliminated.

Step 3. His283 activates water for nucleophilic attack and another oxyanion intermediate is formed.

Step 4. The tetrahedral intermediate collapses and Ser111 is eliminated.

Products.

Contributors

Steven Smith, Gemma L. Holliday, James Willey