3WGC

Aeromonas jandaei L-allo-threonine aldolase H128Y/S292R double mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

L-allo-Threonine aldolase with an H128Y/S292R mutation from Aeromonas jandaei DK-39 reveals the structural basis of changes in substrate stereoselectivity.

Qin, H.M.Imai, F.L.Miyakawa, T.Kataoka, M.Kitamura, N.Urano, N.Mori, K.Kawabata, H.Okai, M.Ohtsuka, J.Hou, F.Nagata, K.Shimizu, S.Tanokura, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1695-1703

  • DOI: https://doi.org/10.1107/S1399004714007664
  • Primary Citation of Related Structures:  
    3WGB, 3WGC

  • PubMed Abstract: 

    L-allo-Threonine aldolase (LATA), a pyridoxal-5'-phosphate-dependent enzyme from Aeromonas jandaei DK-39, stereospecifically catalyzes the reversible interconversion of L-allo-threonine to glycine and acetaldehyde. Here, the crystal structures of LATA and its mutant LATA_H128Y/S292R were determined at 2.59 and 2.50 Å resolution, respectively. Their structures implied that conformational changes in the loop consisting of residues Ala123-Pro131, where His128 moved 4.2 Å outwards from the active site on mutation to a tyrosine residue, regulate the substrate specificity for L-allo-threonine versus L-threonine. Saturation mutagenesis of His128 led to diverse stereoselectivity towards L-allo-threonine and L-threonine. Moreover, the H128Y mutant showed the highest activity towards the two substrates, with an 8.4-fold increase towards L-threonine and a 2.0-fold increase towards L-allo-threonine compared with the wild-type enzyme. The crystal structures of LATA and its mutant LATA_H128Y/S292R reported here will provide further insights into the regulation of the stereoselectivity of threonine aldolases targeted for the catalysis of L-allo-threonine/L-threonine synthesis.


  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-allo-threonine aldolase
A, B, C, D
341Aeromonas jandaeiMutation(s): 2 
Gene Names: LATAltaA
EC: 4.1.2.49
UniProt
Find proteins for O07051 (Aeromonas jandaei)
Explore O07051 
Go to UniProtKB:  O07051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07051
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.78α = 90
b = 93.36β = 113.92
c = 94.02γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description