PDBsum entry 3d5e

Hydrolase

PDB id: 3d5e

Contents

Protein chain

373 a.a. *

Ligands

DEP ×2

FMT ×16

Waters ×288

* Residue conservation analysis

PDB id:

3d5e

Name:

Hydrolase

Title:

Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by paraoxon

Structure:

Platelet-activating factor acetylhydrolase. Chain: a, b. Fragment: unp residues 47-429. Synonym: paf acetylhydrolase, paf 2-acylhydrolase, ldl-associated phospholipase a2, ldl-pla(2), 2-acetyl-1-alkylglycerophosphocholine esterase, 1-alkyl-2-acetylglycerophosphocholine esterase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pla2g7, pafah. Expressed in: escherichia coli.

Resolution:

2.10Å R-factor: 0.207 R-free: 0.261

Authors:

U.Samanta,B.J.Bahnson

Key ref:

U.Samanta and B.J.Bahnson (2008). Crystal Structure of Human Plasma Platelet-activating Factor Acetylhydrolase: STRUCTURAL IMPLICATION TO LIPOPROTEIN BINDING AND CATALYSIS. J Biol Chem, 283, 31617-31624. PubMed id: 18784071 DOI: 10.1074/jbc.M804750200

Date:

16-May-08 Release date: 09-Sep-08

Protein chains

Q13093  (PAFA_HUMAN) -  Platelet-activating factor acetylhydrolase from Homo sapiens

Seq: 441 a.a.

Struc: 373 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.1.47 - 1-alkyl-2-acetylglycerophosphocholine esterase.
• Reaction: a 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H2O = a 1-O-alkyl- sn-glycero-3-phosphocholine + acetate + H⁺

1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H2O = 1-O-alkyl- sn-glycero-3-phosphocholine + acetate (Bound ligand (Het Group name = FMT) matches with 75.00% similarity) + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M804750200

J Biol Chem 283:31617-31624 (2008)

PubMed id: 18784071

Crystal Structure of Human Plasma Platelet-activating Factor Acetylhydrolase: STRUCTURAL IMPLICATION TO LIPOPROTEIN BINDING AND CATALYSIS.

U.Samanta, B.J.Bahnson.

ABSTRACT

Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A(2). The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5A. It has a classic lipase alpha/beta-hydrolase fold, and it contains a catalytic triad of Ser(273), His(351), and Asp(296). Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser(273). The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.

Selected figure(s)

Figure 3.
Polymorphic sites of PAF-AH shown in gray ball and stick relative to the active site Ser^273 and in a view looking directly at the interfacial binding surface of the enzyme. Three of the polymorphic sites (I198T, A379V, and R92H) are solvent-accessible. Two loss of function polymorphisms (V279F and Q281R) that lead to a loss of function in 4% of Japanese individuals are core residues. This figure was rendered using the program PyMOL (51).

Figure 4.
A, model of the tetrahedral intermediate of C(cyan) bound to PAF-AH with catalytic triad residues (Ser^273, His^351, and Asp^296) in green and interfacial-binding residues (Thr^113, His^114, Trp^115, Leu^116, Met^117, Ile^120, Leu^123, Leu^124, Ile^364, Ile^365, Met^368, and Leu^369) in yellow. The coordinates of the tetrahedral intermediate were modeled based on the crystal structure of the DEP moiety complexed to PAF-AH (tetrahedral mimic). The C[18]-alkyl chain was oriented to penetrate into the hydrophobic portion of the LDL particle. The predicted plane of the hydrophilic-hydrophobic interface, which was predicted by the OPM method (47, 48), is displayed with small gray spheres. B, the view from A was rotated by 90° on the y axis to show a side view of the interface and substrate-bound model. A prominent cluster of 10 carboxylate residues (Asp^374, Asp^376, Asp^382, Asp^401, Asp^403, Asp^406, Glu^410, Asp^412, Asp^413, and Glu^414) are shown in red, and three basic residues (Lys^55, Arg^58, and Lys^363) are shown in blue ball and stick. C, electrostatic surface view of A. D, electrostatic surface view of B. The figure was prepared using the program PyMOL (51).

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 31617-31624) copyright 2008.

Figures were selected by an automated process.