4F5M

Wild-Type E. coli Aspartate Aminotransferase: A Template For The Interconversion of Substrate Specificity and Activity To Tyrosine Aminotransferase By The JANUS Algorithm.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Janus: prediction and ranking of mutations required for functional interconversion of enzymes.

Addington, T.A., Mertz, R.W., Siegel, J.B., Thompson, J.M., Fisher, A.J., Filkov, V., Fleischman, N.M., Suen, A.A., Zhang, C., Toney, M.D.

(2013) J.Mol.Biol. 425: 1378-1389

  • DOI: 10.1016/j.jmb.2013.01.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Identification of residues responsible for functional specificity in enzymes is a challenging and important problem in protein chemistry. Active-site residues are generally easy to identify, but residues outside the active site are also important to ...

    Identification of residues responsible for functional specificity in enzymes is a challenging and important problem in protein chemistry. Active-site residues are generally easy to identify, but residues outside the active site are also important to catalysis and their identities and roles are more difficult to determine. We report a method based on analysis of multiple sequence alignments, embodied in our program Janus, for predicting mutations required to interconvert structurally related but functionally distinct enzymes. Conversion of aspartate aminotransferase into tyrosine aminotransferase is demonstrated and compared to previous efforts. Incorporation of 35 predicted mutations resulted in an enzyme with the desired substrate specificity but low catalytic activity. A single round of DNA back-shuffling with wild-type aspartate aminotransferase on this variant generated mutants with tyrosine aminotransferase activities better than those previously realized from rational design or directed evolution. Methods such as this, coupled with computational modeling, may prove invaluable in furthering our understanding of enzyme catalysis and engineering.

    Organizational Affiliation: 

    Department of Chemistry, University of California, Davis, CA 95616, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate aminotransferase
A, B
406Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aspC
EC: 2.6.1.1
Find proteins for P00509 (Escherichia coli (strain K12))
Go to UniProtKB:  P00509
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.299α = 90.00
b = 108.938β = 90.00
c = 144.234γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata collection
PHASERphasing
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Refinement description
  • Version 1.2: 2013-02-27
    Type: Database references
  • Version 1.3: 2013-04-24
    Type: Database references