6H18

Crystal structure of sarin surrogate NIMP inhibited recombinant human bile salt activated lipase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 

Starting Model: experimental
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Literature

X-ray structures of human bile-salt activated lipase conjugated to nerve agents surrogates.

Touvrey, C.Courageux, C.Guillon, V.Terreux, R.Nachon, F.Brazzolotto, X.

(2019) Toxicology 411: 15-23

  • DOI: https://doi.org/10.1016/j.tox.2018.10.015
  • Primary Citation of Related Structures:  
    6H0T, 6H0V, 6H18, 6H19, 6H1A

  • PubMed Abstract: 

    The efficiency of human butyrylcholinesterase (BChE) as a stoichiometric bioscavenger of nerve agents is well established. However, wide use is currently limited by production and purification costs. Aiming at identifying an alternative human protein bioscavenger, we looked for an original scaffold candidate by virtual screening of the Protein Data Bank for functional similarity using the "Surfing the Molecules" software (sumo-pbil.ibcp.fr) and a search model based on the BChE active site topology. Besides the expected acetylcholinesterase and butyrylcholinesterase, we identified a set of bile salt activated lipases structures, among which the human pancreatic lipase (hBAL) that shares 34% identity with BChE. We produced the recombinant enzyme in mammalian cells, purified it, and measured the inhibition constants for paraoxon and surrogates of VX, sarin and tabun. We solved the X-ray structure of apo hBAL and conjugates with paraoxon and the surrogates at resolutions in the 2-Å range. These structures allow the assessment of hBAL for scavenging nerve agents. They revealed that hBAL has inverted stereoselectivity for the surrogates of nerve agent compared to human cholinesterases. We observed a remarkable flip of the catalytic histidine driven by the chelation of Zn 2+ . Dealkylation of the conjugate, aka aging, was solely observed for paraoxon.


  • Organizational Affiliation

    Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, 69367 Lyon Cedex 07, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bile salt-activated lipase547Homo sapiensMutation(s): 2 
Gene Names: CELBAL
EC: 3.1.1.13 (PDB Primary Data), 3.1.1.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P19835 (Homo sapiens)
Explore P19835 
Go to UniProtKB:  P19835
PHAROS:  P19835
GTEx:  ENSG00000170835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19835
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SGB
Query on SGB
A
L-PEPTIDE LINKINGC7 H16 N O5 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.702α = 90
b = 98.055β = 90
c = 110.888γ = 90
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Ministry of Armed ForcesFrancePDH-2-NRBC-3-C-3201
French National Research AgencyFranceASTRID CAT-SCAV

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description