4V15

Crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Crystal Structure of D-Threonine Aldolase from Alcaligenes Xylosoxidans Provides Insight Into a Metal Ion Assisted Plp-Dependent Mechanism.

Uhl, M.K.Oberdorfer, G.Steinkellner, G.Riegler-Berket, L.Mink, D.Van Assema, F.Schurmann, M.Gruber, K.

(2015) PLoS One 10: 24056

  • DOI: 10.1371/journal.pone.0124056
  • Primary Citation of Related Structures:  
    4V15

  • PubMed Abstract: 
  • Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, bu ...

    Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, but the exact physiological function of D-threonine aldolases (DTAs) is still largely unknown. Both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, which are valuable building blocks for the production of pharmaceuticals. While several structures of L-threonine aldolases (LTAs) have already been determined, no structure of a DTA is available to date. Here, we report on the determination of the crystal structure of the DTA from Alcaligenes xylosoxidans (AxDTA) at 1.5 Å resolution. Our results underline the close relationship of DTAs and alanine racemases and allow the identification of a metal binding site close to the PLP-cofactor in the active site of the enzyme which is consistent with the previous observation that divalent cations are essential for DTA activity. Modeling of AxDTA substrate complexes provides a rationale for this metal dependence and indicates that binding of the β-hydroxy group of the substrate to the metal ion very likely activates this group and facilitates its deprotonation by His193. An equivalent involvement of a metal ion has been implicated in the mechanism of a serine dehydratase, which harbors a metal ion binding site in the vicinity of the PLP cofactor at the same position as in DTA. The structure of AxDTA is completely different to available structures of LTAs. The enantio-complementarity of DTAs and LTAs can be explained by an approximate mirror symmetry of crucial active site residues relative to the PLP-cofactor.


    Organizational Affiliation

    Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria; Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010, Graz, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-THREONINE ALDOLASEAB379Achromobacter xylosoxidansMutation(s): 0 
EC: 4.1.2.42
Find proteins for A0A0J9X243 (Alcaligenes xylosoxydans xylosoxydans)
Explore A0A0J9X243 
Go to UniProtKB:  A0A0J9X243
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.267α = 90
b = 84.278β = 111.9
c = 72.852γ = 90
Software Package:
Software NamePurpose
AUTOMARdata reduction
SCALEPACKdata scaling
PHASERphasing
Rosettaphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references