3EJ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.,Sect.D 64: 1277-1282

  • DOI: 10.1107/S0907444908034707
  • Primary Citation of Related Structures:  

  • 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 fu ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-subunit of trans-3-chloroacrylic acid dehalogenase
A, C, E, G, I, K
76Pseudomonas pavonaceaeMutation(s): 0 
Gene Names: caaD1
Find proteins for Q9EV85 (Pseudomonas pavonaceae)
Go to UniProtKB:  Q9EV85
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-subunit of trans-3-chloroacrylic acid dehalogenase
B, D, F, H, J, L
70Pseudomonas pavonaceaeMutation(s): 0 
Gene Names: caaD2
Find proteins for Q9EV84 (Pseudomonas pavonaceae)
Go to UniProtKB:  Q9EV84
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B, J
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, C, E, G, I, K
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.696α = 90.00
b = 97.314β = 96.12
c = 69.022γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
SERGUIdata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance