4X1C

Crystal structure of 4-OT from Pseudomonas putida mt-2 with an enamine adduct on the N-terminal proline at 1.7 Angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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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: 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-hydroxymuconate tautomerase
A, B, D, E, F, I, J, M, N, O
A, B, D, E, F, I, J, M, N, O
62Pseudomonas 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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2-hydroxymuconate tautomeraseC, G, H, K, L62Pseudomonas 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO
Download Ideal Coordinates CCD File 
P [auth B],
Q [auth F]		COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
N80
Query on N80
A, B, D, E, F, I, J, M, N, O
A, B, D, E, F, I, J, M, N, O
L-PEPTIDE LINKINGC7 H11 N O2PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.288α = 90
b = 85.129β = 96.91
c = 170.907γ = 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