6BGN

Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with 5-Fluoro-2-hydroxy-2,4-pentadienoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates.

Stack, T.M.M.Li, W.Johnson, W.H.Zhang, Y.J.Whitman, C.P.

(2018) Biochemistry 57: 1012-1021

  • DOI: 10.1021/acs.biochem.7b00899
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 5-Halo-2-hydroxy-2,4-pentadienoates (5-halo-HPDs) are reportedly generated in the bacterial catabolism of halogenated aromatic hydrocarbons by the meta-fission pathway. The 5-halo-HPDs, where the halogen can be bromide, chloride, or fluoride, result ...

    5-Halo-2-hydroxy-2,4-pentadienoates (5-halo-HPDs) are reportedly generated in the bacterial catabolism of halogenated aromatic hydrocarbons by the meta-fission pathway. The 5-halo-HPDs, where the halogen can be bromide, chloride, or fluoride, result in the irreversible inactivation of 4-oxalocrotonate tautomerase (4-OT), which precedes the enzyme that generates them. The loss of activity is due to the covalent modification of the nucleophilic amino-terminal proline. Mass spectral and crystallographic analysis of the modified enzymes indicates that inactivation of 4-OT by 5-chloro- and 5-bromo-2-hydroxy-2,4-pentadienoate follows a mechanism different from that for the inactivation of 4-OT by 5-fluoro-2-hydroxy-2,4-pentadienoate. The 5-chloro and 5-bromo derivatives undergo 4-OT-catalyzed tautomerization to their respective α,β-unsaturated ketones followed by attack at C5 (by the prolyl nitrogen) with concomitant loss of the halide. For the 5-fluoro species, the presence of a small amount of the α,β-unsaturated ketone could result in a Michael addition of the prolyl nitrogen to C4 followed by protonation at C3. The fluoride is not eliminated. These observations suggest that the inactivation of 4-OT by a downstream metabolite could hamper the efficacy of the pathway, which is the first time that such a bottleneck has been reported for the meta-fission pathway.


    Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-hydroxymuconate tautomerase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
60Pseudomonas putidaMutation(s): 0 
Gene Names: xylH
EC: 5.3.2.6
Find proteins for Q01468 (Pseudomonas putida)
Go to UniProtKB:  Q01468
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6Y5
Query on 6Y5

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
5-fluoranyl-2-oxidanylidene-pentanoic acid
C5 H7 F O3
PKJPKDDIJZVSME-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D, E, F, G, H, I, J, K, L, M, N, O
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
G, H, J
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.116 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.413α = 90.00
b = 88.011β = 98.26
c = 112.674γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection
  • Version 1.2: 2018-06-27
    Type: Data collection, Database references