4KEV | pdb_00004kev

Crystal structure of SsoPox W263L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4KEV

This is version 1.2 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: https://doi.org/10.1371/journal.pone.0075272
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 142.8 kDa 
  • Atom Count: 10,258 
  • 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): 1 
Gene Names: phpphp SSO2522SSO2522
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO

Query on CO



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

Query on FE2



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
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: 2.65 Å
  • R-Value Free:  0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.906α = 90
b = 105.075β = 90
c = 153.888γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary