Phospholipase A2 (group group IVA)

 

Cytosolic phospholipases A2 (cPLA2) are hydrolytic enzymes which catalyse the cleavage of the ester bond at the sn-2 position of phospholipid membranes to generate arachidonic acid, which is the precursor in the metabolic pathway of several lipid messengers, for instance, it is metabolised to prostaglandins by the cyclooxygenase pathway and to leukotrienes by the 5-lipooxygenase pathway. In addition, platelet-activating factor (PAF) can also be generated from a subset of the lysophospholipid produced.

 

Reference Protein and Structure

Sequence
P47712 UniProt (3.1.1.4, 3.1.1.5) IPR002642 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1cjy - HUMAN CYTOSOLIC PHOSPHOLIPASE A2 (2.5 Å) PDBe PDBsum 1cjy
Catalytic CATH Domains
3.40.1090.10 CATHdb (see all for 1cjy)
Click To Show Structure

Enzyme Reaction (EC:3.1.1.4)

1,2-diacyl-sn-glycero-3-phosphocholine
CHEBI:57643ChEBI
+
water
CHEBI:15377ChEBI
→
hydron
CHEBI:15378ChEBI
+
fatty acid anion
CHEBI:28868ChEBI
+
1-O-acyl-sn-glycero-3-phosphocholine
CHEBI:58168ChEBI
Alternative enzyme names: Lecithinase A, Phosphatidase, Phosphatidolipase, Phospholipase A, Phospholipase A2,

Enzyme Mechanism

Introduction

Asp549 acts as a general base, directly activating Ser228. Ser228 acts as a nucleophile to attack the ester bond to form an acyl-enzyme. The developing tetrahedral transition state is stabilised by backbone amide of Gly197 and 198. Arg200 stabilizes the phosphate group. Hydrolysis of the intermediate occurs through an analogous mechanism.

Catalytic Residues Roles

UniProt PDB* (1cjy)
Arg200 Arg200A Stabilizes the phosphate group. electrostatic stabiliser
Ser228 Ser228A It acts as a nucleophile to attack the ester bond to form an acylenzyme intermediate. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor
Gly197 (main-N), Gly198 (main-N) Gly197A (main-N), Gly198A (main-N) It forms an oxyanion hole to stabilise the developing transition state. electrostatic stabiliser
Asp549 Asp549A It acts as a base to activate Ser 228 and a water molecule for nucleophilic attacks. 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. Dessen A (2000), Biochim Biophys Acta, 1488, 40-47. Structure and mechanism of human cytosolic phospholipase A2. DOI:10.1016/s1388-1981(00)00108-6. PMID:11080675.
  2. Wang H et al. (2016), J Mol Biol, 428, 2769-2779. Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition. DOI:10.1016/j.jmb.2016.05.012. PMID:27220631.
  3. Grandits M et al. (2015), J Mol Recognit, 28, 447-457. Selectivity of cytosolic phospholipase A2 type IV toward arachidonyl phospholipids. DOI:10.1002/jmr.2462. PMID:25703463.
  4. Dessen A et al. (1999), Cell, 97, 349-360. Crystal Structure of Human Cytosolic Phospholipase A2 Reveals a Novel Topology and Catalytic Mechanism. DOI:10.1016/s0092-8674(00)80744-8. PMID:10319815.
  5. Huang Z et al. (1996), Biochemistry, 35, 3712-3721. Functional Identification of the Active-Site Nucleophile of the Human 85-kDa Cytosolic Phospholipase A2. DOI:10.1021/bi952541k. PMID:8619991.
  6. Pickard RT et al. (1996), J Biol Chem, 271, 19225-19231. Identification of Essential Residues for the Catalytic Function of 85-kDa Cytosolic Phospholipase A2: PROBING THE ROLE OF HISTIDINE, ASPARTIC ACID, CYSTEINE, AND ARGININE. DOI:10.1074/jbc.271.32.19225. PMID:8702602.

Step 1. Asp549 acts as a general base activating the Ser228 hydroxyl group for nucleophilic attack on the carbonyl carbon of the ester bond. The oxyanion intermediate formed is stabilized by the amide groups of Gly197 and Gly198. Arg200 stabilizes the phosphate group.

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Catalytic Residues Roles

Residue Roles
Ser228A covalently attached
Gly198A (main-N) electrostatic stabiliser
Gly197A (main-N) electrostatic stabiliser
Arg200A electrostatic stabiliser
Asp549A proton acceptor
Ser228A proton donor, nucleophile

Chemical Components

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

Step 2. The tetrahedral intermediate collapses and 1-acyl-sn-glycero-3-phosphocholine is eliminated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser228A covalently attached
Gly197A (main-N) electrostatic stabiliser
Gly198A (main-N) electrostatic stabiliser
Arg200A electrostatic stabiliser
Asp549A proton donor

Chemical Components

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

Step 3. Asp549 activates water for nucleophilic attack and another oxyanion intermediate is formed.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser228A covalently attached
Gly197A (main-N) electrostatic stabiliser
Gly198A (main-N) electrostatic stabiliser
Asp549A proton acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer

Step 4. The tetrahedral intermediate collapses and Ser228 is eliminated.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly197A (main-N) electrostatic stabiliser
Gly198A (main-N) electrostatic stabiliser
Ser228A proton acceptor, nucleofuge
Asp549A 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. Asp549 acts as a general base activating the Ser228 hydroxyl group for nucleophilic attack on the carbonyl carbon of the ester bond. The oxyanion intermediate formed is stabilized by the amide groups of Gly197 and Gly198. Arg200 stabilizes the phosphate group.

Step 2. The tetrahedral intermediate collapses and 1-acyl-sn-glycero-3-phosphocholine is eliminated.

Step 3. Asp549 activates water for nucleophilic attack and another oxyanion intermediate is formed.

Step 4. The tetrahedral intermediate collapses and Ser228 is eliminated.

Products.

Contributors

Mei Leung, Gemma L. Holliday, James Willey