1V04

serum paraoxonase by directed evolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and Evolution of the Serum Paraoxonase Family of Detoxifying and Anti-Atherosclerotic Enzymes

Harel, M.Aharoni, A.Gaidukov, L.Brumshtein, B.Khersonsky, O.Meged, R.Dvir, H.Ravelli, R.B.G.Mccarthy, A.Toker, L.Silman, I.Sussman, J.L.Tawfik, D.S.

(2004) Nat Struct Mol Biol 11: 412

  • DOI: 10.1038/nsmb767
  • Primary Citation of Related Structures:  
    1V04

  • PubMed Abstract: 
  • Members of the serum paraoxonase (PON) family have been identified in mammals and other vertebrates, and in invertebrates. PONs exhibit a wide range of physiologically important hydrolytic activities, including drug metabolism and detoxification of n ...

    Members of the serum paraoxonase (PON) family have been identified in mammals and other vertebrates, and in invertebrates. PONs exhibit a wide range of physiologically important hydrolytic activities, including drug metabolism and detoxification of nerve agents. PON1 and PON3 reside on high-density lipoprotein (HDL, 'good cholesterol') and are involved in the prevention of atherosclerosis. We describe the first crystal structure of a PON family member, a variant of PON1 obtained by directed evolution, at a resolution of 2.2 A. PON1 is a six-bladed beta-propeller with a unique active site lid that is also involved in HDL binding. The three-dimensional structure and directed evolution studies permit a detailed description of PON1's active site and catalytic mechanism, which are reminiscent of secreted phospholipase A2, and of the routes by which PON family members diverged toward different substrate and reaction selectivities.


    Organizational Affiliation

    Department of Structural Biology, The Weizmann Institute of Science, Rehovot 76 100, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERUM PARAOXONASE/ARYLESTERASE 1A355Homo sapiensOryctolagus cuniculusMus musculusRattus rattus
This entity is chimeric
Mutation(s): 0 
EC: 3.1.1.2 (PDB Primary Data), 3.1.8.1 (PDB Primary Data), 3.1.1.81 (UniProt)
Find proteins for P27170 (Oryctolagus cuniculus)
Explore P27170 
Go to UniProtKB:  P27170
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.44α = 90
b = 98.44β = 90
c = 139.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-23
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Source and taxonomy