3DOI

Crystal Structure of a Thermostable Esterase complex with paraoxon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain.

Levisson, M.Sun, L.Hendriks, S.Swinkels, P.Akveld, T.Bultema, J.B.Barendregt, A.van den Heuvel, R.H.H.Dijkstra, B.W.van der Oost, J.Kengen, S.W.M.

(2009) J.Mol.Biol. 385: 949-962

  • DOI: 10.1016/j.jmb.2008.10.075
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima revealed a hypothetical protein (EstA) with typical esterase features. The EstA protein was functionally produced in Escherichia coli and purified to homogeneit ...

    Comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima revealed a hypothetical protein (EstA) with typical esterase features. The EstA protein was functionally produced in Escherichia coli and purified to homogeneity. It indeed displayed esterase activity with optima at or above 95 degrees C and at pH 8.5, with a preference for esters with short acyl chains (C2-C10). Its 2.6-A-resolution crystal structure revealed a classical alpha/beta hydrolase domain with a catalytic triad consisting of a serine, an aspartate, and a histidine. EstA is irreversibly inhibited by the organophosphate paraoxon. A 3.0-A-resolution structure confirmed that this inhibitor binds covalently to the catalytic serine residue of EstA. Remarkably, the structure also revealed the presence of an N-terminal immunoglobulin (Ig)-like domain, which is unprecedented among esterases. EstA forms a hexamer both in the crystal and in solution. Electron microscopy showed that the hexamer in solution is identical with the hexamer in the crystal, which is formed by two trimers, with the N-terminal domains facing each other. Mutational studies confirmed that residues Phe89, Phe112, Phe116, Phe246, and Trp377 affect enzyme activity. A truncated mutant of EstA, in which the Ig-like domain was removed, showed only 5% of wild-type activity, had lower thermostability, and failed to form hexamers. These data suggest that the Ig-like domain plays an important role in the enzyme multimerization and activity of EstA.


    Organizational Affiliation

    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands. Mark.Levisson@wur.nl




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
esterase
A, B
380Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for Q9WXP0 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WXP0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DEP
Query on DEP

Download SDF File 
Download CCD File 
A, B
DIETHYL PHOSPHONATE
C4 H11 O3 P
MJUJXFBTEFXVKU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 130.542α = 90.00
b = 130.542β = 90.00
c = 304.553γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
CNSphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance