1G5F

STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.

Oakley, A.J.Prokop, Z.Bohac, M.Kmunicek, J.Jedlicka, T.Monincova, M.Kuta-Smatanova, I.Nagata, Y.Damborsky, J.Wilce, M.C.

(2002) Biochemistry 41: 4847-4855

  • Primary Citation of Related Structures:  1G42, 1G4H

  • PubMed Abstract: 
  • The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are ...

    The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover. Activity studies showed very weak but detectable activity of LinB with 1,2-dichloroethane [0.012 nmol s(-1) (mg of enzyme)(-1)] and 1,2-dichloropropane [0.027 nmol s(-1) (mg of enzyme)(-1)]. These activities are much weaker compared, for example, to the activity of LinB with 1-chlorobutane [68.2 nmol s(-1) (mg of enzyme)(-1)]. Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane. Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirm that these compounds could bind productively. However, when these moieties were included in the calculations, they bound in a manner similar to that observed in the crystal structure. These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.


    Related Citations: 
    • Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26
      Marek, J.,Vevodova, J.,Smatanova, I.K.,Nagata, Y.,Svensson, L.A.,Newman, J.,Takagi, M.,Damborsky, J.
      (2000) Biochemistry 39: 14082


    Organizational Affiliation

    Department of Pharmacology/Crystallography Centre, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE
A
296Sphingomonas paucimobilisGene Names: linB
EC: 3.8.1.5
Find proteins for P51698 (Sphingomonas paucimobilis)
Go to UniProtKB:  P51698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DCE
Query on DCE

Download SDF File 
Download CCD File 
A
1,2-DICHLOROETHANE
ETHYLENE DICHLORIDE
C2 H4 Cl2
WSLDOOZREJYCGB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
A
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DCEKi: 2310000 nM BINDINGMOAD
DCEKi: 2310000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.860α = 90.00
b = 71.890β = 90.00
c = 73.290γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance