4E3R

PLP-bound aminotransferase mutant crystal structure from Vibrio fluvialis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Redesigning and characterizing the substrate specificity and activity of Vibrio fluvialis aminotransferase for the synthesis of imagabalin.

Midelfort, K.S.Kumar, R.Han, S.Karmilowicz, M.J.McConnell, K.Gehlhaar, D.K.Mistry, A.Chang, J.S.Anderson, M.Villalobos, A.Minshull, J.Govindarajan, S.Wong, J.W.

(2013) Protein Eng.Des.Sel. 26: 25-33

  • DOI: 10.1093/protein/gzs065
  • Primary Citation of Related Structures:  4E3Q

  • PubMed Abstract: 
  • Several protein engineering approaches were combined to optimize the selectivity and activity of Vibrio fluvialis aminotransferase (Vfat) for the synthesis of (3S,5R)-ethyl 3-amino-5-methyloctanoate; a key intermediate in the synthesis of imagabalin, ...

    Several protein engineering approaches were combined to optimize the selectivity and activity of Vibrio fluvialis aminotransferase (Vfat) for the synthesis of (3S,5R)-ethyl 3-amino-5-methyloctanoate; a key intermediate in the synthesis of imagabalin, an advanced candidate for the treatment of generalized anxiety disorder. Starting from wild-type Vfat, which had extremely low activity catalyzing the desired reaction, we engineered an improved enzyme with a 60-fold increase in initial reaction velocity for transamination of (R)-ethyl 5-methyl 3-oxooctanoate to (3S,5R)-ethyl 3-amino-5-methyloctanoate. To achieve this, <450 variants were screened, which allowed accurate assessment of enzyme performance using a low-throughput ultra performance liquid chromatography assay. During the course of this work, crystal structures of Vfat wild type and an improved variant (Vfat variant r414) were solved and they are reported here for the first time. This work also provides insight into the critical residues for substrate specificity for the transamination of (R)-ethyl 5-methyl 3-oxooctanoate and structurally related β-ketoesters.


    Organizational Affiliation

    Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA. Midelfort@msoe.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate transaminase
A, B, C, D
473Vibrio fluvialisN/A
Find proteins for F2XBU9 (Vibrio fluvialis)
Go to UniProtKB:  F2XBU9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.980α = 90.00
b = 161.940β = 90.00
c = 179.270γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
AutoPROCdata collection
AutoPROCdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references