Crystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Crystal structures of native and inactivated cis-3-chloroacrylic acid dehalogenase: Implications for the catalytic and inactivation mechanisms.

Guo, Y.Serrano, H.Johnson, W.H.Ernst, S.Hackert, M.L.Whitman, C.P.

(2011) Bioorg Chem 39: 1-9

  • DOI: https://doi.org/10.1016/j.bioorg.2010.10.001
  • Primary Citation of Related Structures:  
    3MF7, 3MF8

  • PubMed Abstract: 

    The isomeric mixture of cis- and trans-1,3-dichloropropene constitutes the active component of a widely used nematocide known as Telone II®. The mixture is processed by various soil bacteria to acetaldehyde through the 1,3-dichloropropene catabolic pathway. The pathway relies on an isomer-specific hydrolytic dehalogenation reaction catalyzed by cis- or trans-3-chloroacrylic acid dehalogenase, known respectively as cis-CaaD and CaaD. Previous sequence analysis and crystallographic studies of the native and covalently modified enzymes identified Pro-1, His-28, Arg-70, Arg-73, Tyr-103, and Glu-114 as key binding and catalytic residues in cis-CaaD. Mutagenesis of these residues confirmed their importance to the dehalogenation reaction. Crystal structures of the native enzyme (2.01Å resolution) and the enzyme covalently modified at the Pro-1 nitrogen by 2-hydroxypropanoate (1.65Å resolution) are reported here. Both structures are at a resolution higher than previously reported (2.75Å and 2.1Å resolution, respectively). The conformation of the covalent adduct is strikingly different from that previously reported due to its interaction with a 7-residue loop (Thr-32 to Leu-38). The participation of another active site residue, Arg-117, in catalysis and inactivation was also examined. The implications of the combined findings for the mechanisms of catalysis and inactivation are discussed.

  • Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cis-3-chloroacrylic acid dehalogenase149coryneform bacteriumMutation(s): 0 
Gene Names: cis-caaD
EC: 3.8.1
Find proteins for Q6VPE5 (coryneform bacterium)
Explore Q6VPE5 
Go to UniProtKB:  Q6VPE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VPE5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PR4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.783α = 90
b = 96.783β = 90
c = 96.783γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description