4BS0

Crystal Structure of Kemp Eliminase HG3.17 E47N,N300D Complexed with Transition State Analog 6-Nitrobenzotriazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.124 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Precision is Essential for Efficient Catalysis in an Evolved Kemp Eliminase

Blomberg, R.Kries, H.Pinkas, D.M.Mittl, P.R.E.Gruetter, M.G.Privett, H.K.Mayo, S.L.Hilvert, D.

(2013) Nature 503: 418

  • DOI: 10.1038/nature12623

  • PubMed Abstract: 
  • Linus Pauling established the conceptual framework for understanding and mimicking enzymes more than six decades ago. The notion that enzymes selectively stabilize the rate-limiting transition state of the catalysed reaction relative to the bound gro ...

    Linus Pauling established the conceptual framework for understanding and mimicking enzymes more than six decades ago. The notion that enzymes selectively stabilize the rate-limiting transition state of the catalysed reaction relative to the bound ground state reduces the problem of design to one of molecular recognition. Nevertheless, past attempts to capitalize on this idea, for example by using transition state analogues to elicit antibodies with catalytic activities, have generally failed to deliver true enzymatic rates. The advent of computational design approaches, combined with directed evolution, has provided an opportunity to revisit this problem. Starting from a computationally designed catalyst for the Kemp elimination--a well-studied model system for proton transfer from carbon--we show that an artificial enzyme can be evolved that accelerates an elementary chemical reaction 6 × 10(8)-fold, approaching the exceptional efficiency of highly optimized natural enzymes such as triosephosphate isomerase. A 1.09 Å resolution crystal structure of the evolved enzyme indicates that familiar catalytic strategies such as shape complementarity and precisely placed catalytic groups can be successfully harnessed to afford such high rate accelerations, making us optimistic about the prospects of designing more sophisticated catalysts.


    Organizational Affiliation

    1] Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland [2] Corporate RD Division, Firmenich SA, 1211 Geneva, Switzerland (R.B.); Protabit, Pasadena, California 91101, USA (H.K.P.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KEMP ELIMINASE HG3.17
A, B
318Thermoascus aurantiacusMutation(s): 24 
Gene Names: XYNA
EC: 3.2.1.8
Find proteins for P23360 (Thermoascus aurantiacus)
Go to UniProtKB:  P23360
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6NT
Query on 6NT

Download SDF File 
Download CCD File 
A, B
6-NITROBENZOTRIAZOLE
C6 H4 N4 O2
AOCDQWRMYHJTMY-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6NTKi: 2000 nM BINDINGMOAD
6NTKi: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.080α = 90.00
b = 77.950β = 90.00
c = 98.280γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references
  • Version 1.2: 2013-11-27
    Type: Database references