2VC7

Structural basis for natural lactonase and promiscuous phosphotriesterase activities


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

Starting Model: experimental
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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 Biol 379: 1017

  • DOI: https://doi.org/10.1016/j.jmb.2008.04.022
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HT5
Query on HT5

Download Ideal Coordinates CCD File 
BB [auth C],
MA [auth B],
QB [auth D],
Y [auth A]
(4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium
C14 H25 N O2 S
PZUMIWRJDZWNPN-LBPRGKRZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth B]
EB [auth D]
FA [auth B]
G [auth A]
GA [auth B]
BA [auth B],
EB [auth D],
FA [auth B],
G [auth A],
GA [auth B],
HA [auth B],
HB [auth D],
I [auth A],
IB [auth D],
JA [auth B],
K [auth A],
LA [auth B],
LB [auth D],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
PA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
V [auth A],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
ZA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth C]
CA [auth B]
DA [auth B]
EA [auth B]
FB [auth D]
AB [auth C],
CA [auth B],
DA [auth B],
EA [auth B],
FB [auth D],
GB [auth D],
H [auth A],
IA [auth B],
J [auth A],
JB [auth D],
KA [auth B],
KB [auth D],
L [auth A],
MB [auth D],
NB [auth D],
OB [auth D],
PB [auth D],
Q [auth A],
QA [auth C],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
VA [auth C],
YA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
AA [auth B],
DB [auth D],
F [auth A],
OA [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
CB [auth D],
E [auth A],
NA [auth C],
Z [auth B]
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
Binding Affinity Annotations 
IDSourceBinding Affinity
HT5 PDBBind:  2VC7 Ki: 4.33e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.383α = 90
b = 104.124β = 90
c = 153.051γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2020-01-22
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 3.0: 2021-08-18
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Refinement description