PDBsum entry 3f98

Hydrolase

PDB id: 3f98

Contents

Protein chain

377 a.a. *

Ligands

NTJ ×3

FMT ×86

Waters ×1084

* Residue conservation analysis

PDB id:

3f98

Name:

Hydrolase

Title:

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

Structure:

Platelet-activating factor acetylhydrolase. Chain: a, b, c. 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. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.180 R-free: 0.202

Authors:

U.Samanta,B.J.Bahnson

Key ref:

U.Samanta et al. (2009). Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes. Biochem Pharmacol, 78, 420-429. PubMed id: 19394314

Date:

13-Nov-08 Release date: 23-Jun-09

Protein chains

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

Seq: 441 a.a.

Struc: 377 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

Biochem Pharmacol 78:420-429 (2009)

PubMed id: 19394314

Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes.

U.Samanta, S.D.Kirby, P.Srinivasan, D.M.Cerasoli, B.J.Bahnson.

ABSTRACT

The enzyme group-VIIA phospholipase A2 (gVIIA-PLA2) is bound to lipoproteins in human blood and hydrolyzes the ester bond at the sn-2 position of phospholipid substrates with a short sn-2 chain. The enzyme belongs to a serine hydrolase superfamily of enzymes, which react with organophosphorus (OP) nerve agents. OPs ultimately exert their toxicity by inhibiting human acetycholinesterase at nerve synapses, but may additionally have detrimental effects through inhibition of other serine hydrolases. We have solved the crystal structures of gVIIA-PLA2 following inhibition with the OPs diisopropylfluorophosphate, sarin, soman and tabun. The sarin and soman complexes displayed a racemic mix of P(R) and P(S) stereoisomers at the P-chiral center. The tabun complex displayed only the P(R) stereoisomer in the crystal. In all cases, the crystal structures contained intact OP adducts that had not aged. Aging refers to a secondary process OP complexes can go through, which dealkylates the nerve agent adduct and results in a form that is highly resistant to either spontaneous or oxime-mediated reactivation. Non-aged OP complexes of the enzyme were corroborated by trypsin digest and matrix-assisted laser desorption ionization mass spectrometry of OP-enzyme complexes. The lack of stereoselectivity of sarin reaction was confirmed by gas chromatography/mass spectrometry using a chiral column to separate and quantitate the unbound stereoisomers of sarin following incubation with enzyme. The structural details and characterization of nascent reactivity of several toxic nerve agents is discussed with a long-term goal of developing gVIIA-PLA2 as a catalytic bioscavenger of OP nerve agents.