3SRG

Serum paraoxonase-1 by directed evolution at pH 6.5 in complex with 2-hydroxyquinoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1.

Ben-David, M.Elias, M.Filippi, J.J.Dunach, E.Silman, I.Sussman, J.L.Tawfik, D.S.

(2012) J.Mol.Biol. 418: 181-196

  • DOI: 10.1016/j.jmb.2012.02.042
  • Primary Citation of Related Structures:  3SRE

  • PubMed Abstract: 
  • The origins of enzyme specificity are well established. However, the molecular details underlying the ability of a single active site to promiscuously bind different substrates and catalyze different reactions remain largely unknown. To better unders ...

    The origins of enzyme specificity are well established. However, the molecular details underlying the ability of a single active site to promiscuously bind different substrates and catalyze different reactions remain largely unknown. To better understand the molecular basis of enzyme promiscuity, we studied the mammalian serum paraoxonase 1 (PON1) whose native substrates are lipophilic lactones. We describe the crystal structures of PON1 at a catalytically relevant pH and of its complex with a lactone analogue. The various PON1 structures and the analysis of active-site mutants guided the generation of docking models of the various substrates and their reaction intermediates. The models suggest that promiscuity is driven by coincidental overlaps between the reactive intermediate for the native lactonase reaction and the ground and/or intermediate states of the promiscuous reactions. This overlap is also enabled by different active-site conformations: the lactonase activity utilizes one active-site conformation whereas the promiscuous phosphotriesterase activity utilizes another. The hydrolysis of phosphotriesters, and of the aromatic lactone dihydrocoumarin, is also driven by an alternative catalytic mode that uses only a subset of the active-site residues utilized for lactone hydrolysis. Indeed, PON1's active site shows a remarkable level of networking and versatility whereby multiple residues share the same task and individual active-site residues perform multiple tasks (e.g., binding the catalytic calcium and activating the hydrolytic water). Overall, the coexistence of multiple conformations and alternative catalytic modes within the same active site underlines PON1's promiscuity and evolutionary potential.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
serum paraoxonase
A
355N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
OCH
Query on OCH

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A
QUINOLIN-2(1H)-ONE
2-OXOQUINOLINE
C9 H7 N O
LISFMEBWQUVKPJ-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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A
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OCHKi: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.544α = 90.00
b = 93.544β = 90.00
c = 144.621γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references