4Q1U

Serum paraoxonase-1 by directed evolution with the K192Q mutation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Catalytic stimulation by restrained active-site floppiness-the case of high density lipoprotein-bound serum paraoxonase-1.

Ben-David, M., Sussman, J.L., Maxwell, C.I., Szeler, K., Kamerlin, S.C., Tawfik, D.S.

(2015) J Mol Biol 427: 1359-1374

  • DOI: 10.1016/j.jmb.2015.01.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Despite the abundance of membrane-associated enzymes, the mechanism by which membrane binding stabilizes these enzymes and stimulates their catalysis remains largely unknown. Serum paraoxonase-1 (PON1) is a lipophilic lactonase whose stability and en ...

    Despite the abundance of membrane-associated enzymes, the mechanism by which membrane binding stabilizes these enzymes and stimulates their catalysis remains largely unknown. Serum paraoxonase-1 (PON1) is a lipophilic lactonase whose stability and enzymatic activity are dramatically stimulated when associated with high-density lipoprotein (HDL) particles. Our mutational and structural analyses, combined with empirical valence bond simulations, reveal a network of hydrogen bonds that connect HDL binding residues with Asn168--a key catalytic residue residing >15Å from the HDL contacting interface. This network ensures precise alignment of N168, which, in turn, ligates PON1's catalytic calcium and aligns the lactone substrate for catalysis. HDL binding restrains the overall motion of the active site and particularly of N168, thus reducing the catalytic activation energy barrier. We demonstrate herein that disturbance of this network, even at its most far-reaching periphery, undermines PON1's activity. Membrane binding thus immobilizes long-range interactions via second- and third-shell residues that reduce the active site's floppiness and pre-organize the catalytic residues. Although this network is critical for efficient catalysis, as demonstrated here, unraveling these long-rage interaction networks is challenging, let alone their implementation in artificial enzyme design.

    Organizational Affiliation: 

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address: tawfik@weizmann.ac.il.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum paraoxonase/arylesterase 1
A
355hybridMutation(s): 0 
EC: 3.1.1.2 (PDB Primary Data), 3.1.1.81 (PDB Primary Data), 3.1.8.1 (PDB Primary Data)
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT
Download CCD File 
A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
BR
Query on BR
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.514α = 90
b = 93.514β = 90
c = 144.007γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references