1-alkyl-2-acetylglycerophosphocholine esterase

 

2-acetyl-1-alkylglycerophosphocholine esterase, also known as known as platelet-activating factor acetylhydrolase (PAF-AH).

Mammalian brain contains significant levels of platelet activating-factor (PAF), these act as a synapse messenger and transcription inducer of the early response genes c-fos and c-jun. The platelet-activating factor PAF is a potent lipid first messenger active in general cell activation, fertilisation, inflammatory and allergic reactions, asthma, HIV pathogenesis, carcinogenesis, and apoptosis. PAF has also been implicated as a messenger in long-term potentiation, a cellular model of memory formation.

Inactivation of this factor is carried out by PAF-AH, a subfamily of phospholipases A2 that remove the sn-2 acetyl group. Mammalian brain contains at least three intracellular isoforms, 1b being the best characterised. From experimentation it can be assumed that PAF-AH maintains the PAF concentration within a certain range during brain development.

The protein is an unusual G-protein like (alpha1/alpha2)beta trimer. PAF-AH is a heterotrimer composed of 26-,26-, and 45-Kda polypeptides. The alpha (26KDa) is the catalytic subunit. The active site is made up of a trypsin-like triad of Ser 47, His 195 and Asp 192. The other subunit is not essential for the catalytic activity. The catalytic subunit contains a single alpha/beta domain with a central, parallel, 6-stranded beta sheet. This fold is very like that found in GTPase. Experimental data has demonstrated that the catalytic subunit of brain PAF acetylhydrolase is a novel type of serine esterase.

 

Reference Protein and Structure

Sequence
Q29460 UniProt (3.1.1.47) IPR013830 (Sequence Homologues) (PDB Homologues)
Biological species
Bos taurus (Cattle) Uniprot
PDB
1wab - PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE (1.7 Å) PDBe PDBsum 1wab
Catalytic CATH Domains
3.40.50.1110 CATHdb (see all for 1wab)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.47)

water
CHEBI:15377ChEBI
+
2-acetyl-1-alkyl-sn-glycero-3-phosphocholine
CHEBI:36707ChEBI
→
acetate
CHEBI:30089ChEBI
+
1-alkyl-sn-glycero-3-phosphocholine
CHEBI:30909ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase, Alkylacetyl-GPC:acetylhydrolase, LDL-associated phospholipase A(2), PAF acetylhydrolase, LDL-PLA(2), PAF 2-acylhydrolase, Platelet-activating factor acetylhydrolase, 2-acetyl-1-alkylglycerophosphocholine esterase,

Enzyme Mechanism

Introduction

Ser47 is close to His195, the imidazole ring of His195 is hydrogen-bonded through its nitrogen (delta 1) atom to the side-chain carboxyl of Asp192. This forms a classical Ser-His-Asp triad, and Ser47 is thought to be the catalytic nucleophile. The chirality of the triad is the same as that found in the active sites of other esterases and neutral lipases, where nucleophilic attack is on the re face of the ester. The main chain amide of Gly74 and Nd1 of Asn104 stabilise oxyanion hole.

Catalytic Residues Roles

UniProt PDB* (1wab)
Ser47 Ser47A Acts as the catalytic nucleophile. covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleophile, nucleofuge, proton donor, proton acceptor
Gly74 (main-N), Asn104 Gly74A (main-N), Asn104A Forms the oxyanion hole. hydrogen bond donor, electrostatic stabiliser
Asp192 Asp192A Activates His195 to act as the general acid/base, forms part of the Ser-His-Asp triad. activator, hydrogen bond acceptor, electrostatic stabiliser
His195 His195A Acts as a general acid/base, forms part of the Ser-His-Asp triad. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, 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, bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation, intermediate formation, unimolecular elimination by the conjugate base, overall product formed, enzyme-substrate complex cleavage, intermediate collapse, native state of enzyme regenerated, intermediate terminated

References

  1. Ho YS et al. (1997), Nature, 385, 89-93. Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer. DOI:10.1038/385089a0. PMID:8985254.
  2. Epstein TM et al. (2009), Biochemistry, 48, 3425-3435. Crystal Structures of Brain Group-VIII Phospholipase A2 in Nonaged Complexes with the Organophosphorus Nerve Agents Soman and Sarin†,‡. DOI:10.1021/bi8023527. PMID:19271773.
  3. McIntyre TM et al. (2009), J Lipid Res, 50, S255-S259. The emerging roles of PAF acetylhydrolase. DOI:10.1194/jlr.r800024-jlr200. PMID:18838739.
  4. Karasawa K et al. (2003), Prog Lipid Res, 42, 93-114. Plasma platelet activating factor-acetylhydrolase (PAF-AH). PMID:12547653.
  5. McMullen TW et al. (2000), Protein Eng, 13, 865-871. The functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib). PMID:11239086.
  6. Ho YS et al. (1999), Protein Eng, 12, 693-700. Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. DOI:10.2210/pdb1bwr/pdb. PMID:10469831.
  7. Hattori M et al. (1994), J Biol Chem, 269, 23150-23155. The catalytic subunit of bovine brain platelet-activating factor acetylhydrolase is a novel type of serine esterase. PMID:8083218.

Step 1. His195 deprotonates Ser47.

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Catalytic Residues Roles

Residue Roles
Asp192A hydrogen bond acceptor, activator
Gly74A (main-N) hydrogen bond donor
Asn104A hydrogen bond donor
His195A hydrogen bond acceptor, hydrogen bond donor
Ser47A hydrogen bond donor
His195A proton acceptor
Ser47A proton donor

Chemical Components

proton transfer

Step 2. Ser47 initiates a nucleophilic attack upon the carbonyl carbon of the substrate in an addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp192A hydrogen bond acceptor, electrostatic stabiliser
Gly74A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn104A hydrogen bond donor, electrostatic stabiliser
His195A hydrogen bond donor, electrostatic stabiliser
Ser47A hydrogen bond acceptor, nucleophile

Chemical Components

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

Step 3. The oxyanion formed collapses, eliminating phosphocholine with concomitant deprotonation of His195.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp192A hydrogen bond acceptor, electrostatic stabiliser
Gly74A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn104A hydrogen bond donor, electrostatic stabiliser
His195A hydrogen bond donor, hydrogen bond acceptor
Ser47A covalently attached, hydrogen bond acceptor
His195A proton donor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base, overall product formed, enzyme-substrate complex cleavage, intermediate collapse, intermediate formation

Step 4. His195 deprotonates water, which initiates a nucleophilic attack upon the carbonyl carbon of the acyl-intermediate in an addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp192A hydrogen bond acceptor
Gly74A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn104A hydrogen bond donor, electrostatic stabiliser
His195A hydrogen bond donor, hydrogen bond acceptor
Ser47A covalently attached
His195A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation, intermediate formation

Step 5. The oxyanion collapses, eliminating Ser47 with concomitant deprotonation of His195.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp192A hydrogen bond acceptor, electrostatic stabiliser
Gly74A (main-N) hydrogen bond donor, electrostatic stabiliser
Asn104A hydrogen bond donor, electrostatic stabiliser
His195A hydrogen bond donor
Ser47A hydrogen bond acceptor
His195A proton donor
Ser47A nucleofuge, proton acceptor

Chemical Components

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

Step 1. His195 deprotonates Ser47.

Step 2. Ser47 initiates a nucleophilic attack upon the carbonyl carbon of the substrate in an addition reaction.

Step 3. The oxyanion formed collapses, eliminating phosphocholine with concomitant deprotonation of His195.

Step 4. His195 deprotonates water, which initiates a nucleophilic attack upon the carbonyl carbon of the acyl-intermediate in an addition reaction.

Step 5. The oxyanion collapses, eliminating Ser47 with concomitant deprotonation of His195.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Nozomi Nagano, Craig Porter, Marko Babić