4X19

Crystal structure of native 4-OT from Pseudomonas putida mt-2 at 1.94 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence for the Formation of an Enamine Species during Aldol and Michael-type Addition Reactions Promiscuously Catalyzed by 4-Oxalocrotonate Tautomerase.

Poddar, H.Rahimi, M.Geertsema, E.M.Thunnissen, A.M.Poelarends, G.J.

(2015) Chembiochem 16: 738-741

  • DOI: https://doi.org/10.1002/cbic.201402687
  • Primary Citation of Related Structures:  
    4X19, 4X1C

  • PubMed Abstract: 

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable γ-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate.


  • Organizational Affiliation

    Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen (The Netherlands).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-hydroxymuconate tautomerase62Pseudomonas putidaMutation(s): 0 
Gene Names: xylH
EC: 5.3.2.6
UniProt
Find proteins for Q01468 (Pseudomonas putida)
Explore Q01468 
Go to UniProtKB:  Q01468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01468
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download Ideal Coordinates CCD File 
EA [auth F]COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.48α = 90
b = 88.816β = 94.51
c = 169.877γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council242293

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description