2O7V

Carboxylesterase AeCXE1 from Actinidia eriantha covalently inhibited by paraoxon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

High-Resolution Crystal Structure of Plant Carboxylesterase AeCXE1, from Actinidia eriantha, and Its Complex with a High-Affinity Inhibitor Paraoxon.

Ileperuma, N.R.Marshall, S.D.Squire, C.J.Baker, H.M.Oakeshott, J.G.Russell, R.J.Plummer, K.M.Newcomb, R.D.Baker, E.N.

(2007) Biochemistry 46: 1851-1859

  • DOI: https://doi.org/10.1021/bi062046w
  • Primary Citation of Related Structures:  
    2O7R, 2O7V

  • PubMed Abstract: 

    Carboxylesterases (CXEs) are widely distributed in plants, where they have been implicated in roles that include plant defense, plant development, and secondary metabolism. We have cloned, overexpressed, purified, and crystallized a carboxylesterase from the kiwifruit species Actinidia eriantha (AeCXE1). The structure of AeCXE1 was determined by X-ray crystallography at 1.4 A resolution. The crystal structure revealed that AeCXE1 is a member of the alpha/beta-hydrolase fold superfamily, most closely related structurally to the hormone-sensitive lipase subgroup. The active site of the enzyme, located in an 11 A deep hydrophobic gorge, contains the conserved catalytic triad residues Ser169, Asp276, and His306. Kinetic analysis using artificial ester substrates showed that the enzyme can hydrolyze a range of carboxylester substrates with acyl groups ranging from C2 to C16, with a preference for butyryl moieties. This preference was supported by the discovery of a three-carbon acyl adduct bound to the active site Ser169 in the native structure. AeCXE1 was also found to be inhibited by organophosphates, with paraoxon (IC50 = 1.1 muM) a more potent inhibitor than dimethylchlorophosphate (DMCP; IC50 = 9.2 muM). The structure of AeCXE1 with paraoxon bound was determined at 2.3 A resolution and revealed that the inhibitor binds covalently to the catalytic serine residue, with virtually no change in the structure of the enzyme. The structural information for AeCXE1 provides a basis for addressing the wider functional roles of carboxylesterases in plants.


  • Organizational Affiliation

    School of Biological Sciences, University of Auckland, Auckland, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CXE carboxylesterase338Actinidia erianthaMutation(s): 0 
Gene Names: CXE1
EC: 3.1.1.1
UniProt
Find proteins for Q0ZPV7 (Actinidia eriantha)
Explore Q0ZPV7 
Go to UniProtKB:  Q0ZPV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZPV7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DEP
Query on DEP

Download Ideal Coordinates CCD File 
B [auth A]DIETHYL PHOSPHONATE
C4 H11 O3 P
MJUJXFBTEFXVKU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DEP PDBBind:  2O7V IC50: 1100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.078α = 90
b = 53.908β = 102.21
c = 42.366γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Refinement description
  • Version 1.6: 2024-10-16
    Changes: Structure summary