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

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.118 

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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: https://doi.org/10.1021/acs.biochem.7b00899
  • Primary Citation of Related Structures:  
    5TIG, 6BGN

  • 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 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

    Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-hydroxymuconate tautomerase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
60Pseudomonas putidaMutation(s): 0 
Gene Names: xylH
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6Y5

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
GA [auth H]
KA [auth I]
MA [auth J]
AA [auth F],
CA [auth G],
GA [auth H],
KA [auth I],
MA [auth J],
P [auth A],
PA [auth K],
Q [auth B],
RA [auth L],
TA [auth M],
U [auth C],
V [auth D],
VA [auth N],
XA [auth O],
Y [auth E]
5-fluoranyl-2-oxidanylidene-pentanoic acid
C5 H7 F O3
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
EA [auth G]
HA [auth H]
IA [auth H]
BA [auth F],
DA [auth G],
EA [auth G],
HA [auth H],
IA [auth H],
LA [auth I],
NA [auth J],
QA [auth K],
R [auth B],
S [auth B],
SA [auth L],
T [auth B],
UA [auth M],
W [auth D],
WA [auth N],
X [auth D],
YA [auth O],
Z [auth E]
C3 H8 O3
Query on NO3

Download Ideal Coordinates CCD File 
FA [auth G],
JA [auth H],
OA [auth J]
N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.118 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.413α = 90
b = 88.011β = 98.26
c = 112.674γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence