5EKY

Crystal structure of deoxyribose-phosphate aldolase from Escherichia coli (K58E-Y96W mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Mechanism-based inhibition of an aldolase at high concentrations of its natural substrate acetaldehyde: structural insights and protective strategies.

Dick, M.Hartmann, R.Weiergraber, O.H.Bisterfeld, C.Classen, T.Schwarten, M.Neudecker, P.Willbold, D.Pietruszka, J.

(2016) Chem Sci 7: 4492-4502

  • DOI: 10.1039/c5sc04574f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance ...

    2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is used in organic synthesis for the enantioselective reaction between acetaldehyde and a broad range of other aldehydes as acceptor molecules. Nevertheless, its application is hampered by a poor tolerance towards high concentrations of acetaldehyde, its natural substrate. While numerous studies have been performed searching for new, more acetaldehyde-resistant DERAs, the mechanism underlying this deactivation process has remained elusive. By using NMR spectroscopy on both the protein and the small-molecule scale, we could show that a reaction product binds to the inner part of the enzyme, and that this effect can be partly reversed via heating. The crystal structure of DERA before and after acetaldehyde incubation was determined at high resolution, revealing a covalently bound reaction product bridging the catalytically active lysine (K167) to a nearby cysteine (C47) in the deactivated enzyme. A reaction mechanism is proposed where crotonaldehyde as the aldol product of two acetaldehyde molecules after water elimination forms a Schiff base with the lysine side chain, followed by Michael addition of the cysteine thiol group to the C β atom of the inhibitor. In support of this mechanism, direct incubation of DERA with crotonaldehyde results in a more than 100-fold stronger inhibition, compared to acetaldehyde, whereas mutation of C47 gives rise to a fully acetaldehyde-resistant DERA. Thus this variant appears perfectly suited for synthetic applications. A similar diagnostic and preventive strategy should be applicable to other biocatalysts suffering from mechanism-based inhibition by a reactive substrate, a condition that may be more common than currently appreciated in biotechnology.


    Organizational Affiliation

    Institute of Bioorganic Chemistry , Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich , 52426 Jülich , Germany . Email: j.pietruszka@fz-juelich.de.,Institute of Bio- and Geosciences , IBG-1: Biotechnology , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institut für Physikalische Biologie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany.,Institute of Complex Systems , ICS-6: Structural Biochemistry , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyribose-phosphate aldolase
A
265Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: deoC (dra, thyR)
EC: 4.1.2.4
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
BU2
Query on BU2

Download SDF File 
Download CCD File 
A
1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.121 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.790α = 90.00
b = 53.360β = 98.30
c = 37.840γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 2.0: 2018-09-12
    Type: Atomic model, Data collection, Database references