4ZP1

Crystal structure of Zymomonas mobilis pyruvate decarboxylase variant Glu473Ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.205 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tuning and Switching Enantioselectivity of Asymmetric Carboligation in an Enzyme through Mutational Analysis of a Single Hot Spot.

Wechsler, C.Meyer, D.Loschonsky, S.Funk, L.M.Neumann, P.Ficner, R.Brodhun, F.Muller, M.Tittmann, K.

(2015) Chembiochem 16: 2580-2584

  • DOI: 10.1002/cbic.201500529

  • PubMed Abstract: 
  • Enantioselective bond making and breaking is a hallmark of enzyme action, yet switching the enantioselectivity of the reaction is a difficult undertaking, and typically requires extensive screening of mutant libraries and multiple mutations. Here, we ...

    Enantioselective bond making and breaking is a hallmark of enzyme action, yet switching the enantioselectivity of the reaction is a difficult undertaking, and typically requires extensive screening of mutant libraries and multiple mutations. Here, we demonstrate that mutational diversification of a single catalytic hot spot in the enzyme pyruvate decarboxylase gives access to both enantiomers of acyloins acetoin and phenylacetylcarbinol, important pharmaceutical precursors, in the case of acetoin even starting from the unselective wild-type protein. Protein crystallography was used to rationalize these findings and to propose a mechanistic model of how enantioselectivity is controlled. In a broader context, our studies highlight the efficiency of mechanism-inspired and structure-guided rational protein design for enhancing and switching enantioselectivity of enzymatic reactions, by systematically exploring the biocatalytic potential of a single hot spot.


    Organizational Affiliation

    Abt. Molekulare Enzymologie, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany. ktittma@gwdg.de.,Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany.,Abt. Molekulare Enzymologie, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.,Abt. Molekulare Strukturbiologie, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate decarboxylase
A, B, C, D
568Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)Mutation(s): 1 
Gene Names: pdc
EC: 4.1.1.1
Find proteins for P06672 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Go to UniProtKB:  P06672
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C, D
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.205 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.290α = 90.00
b = 167.640β = 101.66
c = 110.820γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR 1296/TP3

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence