1G5F

STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 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

  • DOI: 10.1021/bi015734i
  • Primary Citation of Related Structures:  
    1G42, 1G4H, 1G5F

  • 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 to be utilized for bioremediation of organohalide-contaminated industrial waste ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE A296Sphingomonas paucimobilisMutation(s): 1 
Gene Names: linB
EC: 3.8.1 (PDB Primary Data), 3.8.1.5 (UniProt)
Find proteins for D4Z2G1 (Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S))
Explore D4Z2G1 
Go to UniProtKB:  D4Z2G1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCE
Query on DCE

Download Ideal Coordinates CCD File 
A
1,2-DICHLOROETHANE
C2 H4 Cl2
WSLDOOZREJYCGB-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
AL-PEPTIDE LINKINGC8 H18 N4 O2ARG
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DCEKi:  2310000   nM  Binding MOAD
DCEKi :  2310000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.86α = 90
b = 71.89β = 90
c = 73.29γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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