3U1O

THREE DIMENSIONAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH19, Northeast Structural Genomics Consortium Target OR49


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.494 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 

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 design cysteine esterase ECH19
A, B
419N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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: 2.494 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 109.135α = 90.00
b = 129.200β = 90.00
c = 72.178γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
ADSCdata collection
PHENIXrefinement
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references