3EJ9

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic analysis of trans-3-chloroacrylic acid dehalogenase activity.

Pegan, S.D.Serrano, H.Whitman, C.P.Mesecar, A.D.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1277-1282

  • DOI: 10.1107/S0907444908034707
  • Primary Citation of Related Structures:  
    3EJ3, 3EJ7, 3EJ9

  • PubMed Abstract: 
  • Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source ...

    Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic betaPro1 residue. Here, the 1.7 A resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain alphaGlu52 is observed in the structure, supporting its role in the catalytic mechanism.


    Organizational Affiliation

    Center of Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, USA. pegan@uic.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-subunit of trans-3-chloroacrylic acid dehalogenaseA, C, E76Pseudomonas pavonaceaeMutation(s): 1 
Gene Names: caaD1
EC: 5.3.2.6
UniProt
Find proteins for Q9EV85 (Pseudomonas pavonaceae)
Explore Q9EV85 
Go to UniProtKB:  Q9EV85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EV85
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-subunit of trans-3-chloroacrylic acid dehalogenaseB, D, F70Pseudomonas pavonaceaeMutation(s): 0 
Gene Names: caaD2
EC: 5.3.2.6
UniProt
Find proteins for Q9EV84 (Pseudomonas pavonaceae)
Explore Q9EV84 
Go to UniProtKB:  Q9EV84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EV84
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.28α = 90
b = 69.67β = 90
c = 89.885γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references