4KET

Crystal structure of SsoPox W263I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


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


Literature

Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox.

Hiblot, J., Gotthard, G., Elias, M., Chabriere, E.

(2013) PLoS One 8: e75272-e75272

  • DOI: 10.1371/journal.pone.0075272
  • Primary Citation of Related Structures:  
    4KER, 4KES, 4KET, 4KEU, 4KEV, 4KEZ, 4KF1

  • PubMed Abstract: 

    • Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions ...

    Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.

    Organizational Affiliation: 

    URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AryldialkylphosphataseA, B, C, D314Saccharolobus solfataricusMutation(s): 1 
Gene Names: php, php SSO2522, SSO2522
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4
Download Ideal Coordinates CCD File 
CA [auth D],
V [auth C]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
R [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
DA [auth D],
FA [auth D],
H [auth A],
I [auth A],
J [auth A],
DA [auth D],
FA [auth D],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
W [auth C],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
BA [auth D],
EA [auth D],
G [auth A],
GA [auth D],
K [auth A],
BA [auth D],
EA [auth D],
G [auth A],
GA [auth D],
K [auth A],
L [auth B],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CO
Query on CO
Download Ideal Coordinates CCD File 
AA [auth D],
F [auth A],
N [auth B],
T [auth C]		COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
S [auth C],
Z [auth D]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.00 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.4α = 90
b = 103.9β = 90
c = 150.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-11-20
    Changes: Database references