2VC5 | pdb_00002vc5

Structural basis for natural lactonase and promiscuous phosphotriesterase activities


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.282 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2VC5

This is version 2.1 of the entry. See complete history

Literature

Structural Basis for Natural Lactonase and Promiscuous Phosphotriesterase Activities.

Elias, M.Dupuy, J.Merone, L.Mandrich, L.Porzio, E.Moniot, S.Rochu, D.Lecomte, C.Rossi, M.Masson, P.Manco, G.Chabriere, E.

(2008) J Mol Biology 379: 1017

  • DOI: https://doi.org/10.1016/j.jmb.2008.04.022
  • Primary Citation Related Structures: 
    2VC5, 2VC7

  • PubMed Abstract: 

    Organophosphates are the largest class of known insecticides, several of which are potent nerve agents. Consequently, organophosphate-degrading enzymes are of great scientific interest as bioscavengers and biodecontaminants. Recently, a hyperthermophilic phosphotriesterase (known as SsoPox), from the Archaeon Sulfolobus solfataricus, has been isolated and found to possess a very high lactonase activity. Here, we report the three-dimensional structures of SsoPox in the apo form (2.6 A resolution) and in complex with a quorum-sensing lactone mimic at 2.0 A resolution. The structure also reveals an unexpected active site topology, and a unique hydrophobic channel that perfectly accommodates the lactone substrate. Structural and mutagenesis evidence allows us to propose a mechanism for lactone hydrolysis and to refine the catalytic mechanism established for phosphotriesterases. In addition, SsoPox structures permit the correlation of experimental lactonase and phosphotriesterase activities and this strongly suggests lactonase activity as the cognate function of SsoPox. This example demonstrates that promiscuous activities probably constitute a large and efficient reservoir for the creation of novel catalytic activities.


  • Organizational Affiliation
    • Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS-Université Henri Poincaré, 54506 Nancy, France.

Macromolecule Content 

  • Total Structure Weight: 144.57 kDa 
  • Atom Count: 10,475 
  • Modeled Residue Count: 1,256 
  • Deposited Residue Count: 1,256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ARYLDIALKYLPHOSPHATASE
A, B, C, D
314Saccharolobus solfataricusMutation(s): 0 
EC: 3.1.8.1
UniProt
Find proteins for Q97VT7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97VT7 
Go to UniProtKB:  Q97VT7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97VT7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
EA [auth D]
H [auth A]
K [auth A]
O [auth B]
P [auth B]
EA [auth D],
H [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
CA [auth D]
DA [auth D]
FA [auth D]
G [auth A]
GA [auth D]
CA [auth D],
DA [auth D],
FA [auth D],
G [auth A],
GA [auth D],
I [auth A],
J [auth A],
N [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO

Query on CO



Download:Ideal Coordinates CCD File
BA [auth D],
F [auth A],
M [auth B],
W [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
AA [auth D],
E [auth A],
L [auth B],
V [auth C]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.16α = 90
b = 104.82β = 90
c = 155.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-08-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Refinement description