3F98

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

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

(2009) Biochem Pharmacol 78: 420-429

  • DOI: 10.1016/j.bcp.2009.04.018
  • Primary Citation of Related Structures:  
    3F96, 3F97, 3F98, 3F9C

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolaseA, B, C383Homo sapiensMutation(s): 0 
Gene Names: PLA2G7PAFAH
EC: 3.1.1.47
UniProt & NIH Common Fund Data Resources
Find proteins for Q13093 (Homo sapiens)
Explore Q13093 
Go to UniProtKB:  Q13093
PHAROS:  Q13093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13093
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NTJ
Query on NTJ

Download Ideal Coordinates CCD File 
D [auth A],
JA [auth B],
LB [auth C]
R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
C4 H12 N O2 P
VJBIKDDUGQICEU-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth B],
AC [auth C],
BA [auth A],
BB [auth B],
AA [auth A],
AB [auth B],
AC [auth C],
BA [auth A],
BB [auth B],
BC [auth C],
CA [auth A],
CB [auth B],
CC [auth C],
DA [auth A],
DB [auth B],
DC [auth C],
E [auth A],
EA [auth A],
EB [auth B],
EC [auth C],
F [auth A],
FA [auth A],
FB [auth B],
FC [auth C],
G [auth A],
GA [auth A],
GB [auth B],
GC [auth C],
H [auth A],
HA [auth A],
HB [auth B],
HC [auth C],
I [auth A],
IA [auth A],
IB [auth B],
IC [auth C],
J [auth A],
JB [auth B],
JC [auth C],
K [auth A],
KA [auth B],
KB [auth B],
KC [auth C],
L [auth A],
LA [auth B],
LC [auth C],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth C],
N [auth A],
NA [auth B],
NB [auth C],
NC [auth C],
O [auth A],
OA [auth B],
OB [auth C],
P [auth A],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
R [auth A],
RA [auth B],
RB [auth C],
S [auth A],
SA [auth B],
SB [auth C],
T [auth A],
TA [auth B],
TB [auth C],
U [auth A],
UA [auth B],
UB [auth C],
V [auth A],
VA [auth B],
VB [auth C],
W [auth A],
WA [auth B],
WB [auth C],
X [auth A],
XA [auth B],
XB [auth C],
Y [auth A],
YA [auth B],
YB [auth C],
Z [auth A],
ZA [auth B],
ZB [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.984α = 90
b = 133.322β = 90
c = 253.855γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance