3UAK

Crystal Structure of De Novo designed cysteine esterase ECH14, Northeast Structural Genomics Consortium Target OR54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.232 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.

Richter, F.Blomberg, R.Khare, S.D.Kiss, G.Kuzin, A.P.Smith, A.J.Gallaher, J.Pianowski, Z.Helgeson, R.C.Grjasnow, A.Xiao, R.Seetharaman, J.Su, M.Vorobiev, S.Lew, S.Forouhar, F.Kornhaber, G.J.Hunt, J.F.Montelione, G.T.Tong, L.Houk, K.N.Hilvert, D.Baker, D.

(2012) J.Am.Chem.Soc. 134: 16197-16206

  • DOI: 10.1021/ja3037367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is dif ...

    Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
De Novo designed cysteine esterase ECH14
A, B
406N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.232 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.645α = 90.00
b = 81.814β = 90.00
c = 159.714γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
BALBESphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACrefinement
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references