5HHT

Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.

Affaticati, P.E.Dai, S.B.Payongsri, P.Hailes, H.C.Tittmann, K.Dalby, P.A.

(2016) Sci Rep 6: 35716-35716

  • DOI: 10.1038/srep35716

  • PubMed Abstract: 
  • The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acc ...

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.


    Organizational Affiliation

    Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transketolase 1
A, B
669Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: tktA (tkt)
EC: 2.2.1.1
Find proteins for P27302 (Escherichia coli (strain K12))
Go to UniProtKB:  P27302
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

Download SDF File 
Download CCD File 
A, B
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 89.944α = 90.00
b = 102.044β = 90.00
c = 133.076γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-11 
  • Released Date: 2016-11-02 
  • Deposition Author(s): Dai, S., Tittmann, K.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR 1296/TP 3

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Data collection