3U0S

Crystal Structure of an Enzyme Redesigned Through Multiplayer Online Gaming: CE6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

Eiben, C.B.Siegel, J.B.Bale, J.B.Cooper, S.Khatib, F.Shen, B.W.Players, F.Stoddard, B.L.Popovic, Z.Baker, D.

(2012) Nat.Biotechnol. 30: 190-192

  • DOI: 10.1038/nbt.2109

  • PubMed Abstract: 
  • Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we ...

    Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.


    Related Citations: 
    • Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris.
      Scharff, E.I.,Koepke, J.,Fritzsch, G.,Lucke, C.,Ruterjans, H.
      (2001) Structure 9: 493
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.
      Siegel, J.B.,Zanghellini, A.,Lovick, H.M.,Kiss, G.,Lambert, A.R.,St Clair, J.L.,Gallaher, J.L.,Hilvert, D.,Gelb, M.H.,Stoddard, B.L.,Houk, K.N.,Michael, F.E.,Baker, D.
      (2010) Science 329: 309


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diisopropyl-fluorophosphatase
A, B
337Loligo vulgarisMutation(s): 15 
EC: 3.1.8.2
Find proteins for Q7SIG4 (Loligo vulgaris)
Go to UniProtKB:  Q7SIG4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 87.002α = 90.00
b = 87.002β = 90.00
c = 163.330γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description