4H7K

Crystal structure of haloalkane dehalogenase LinB I253M mutant from Sphingobium sp. MI1205


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Literature

Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.

Okai, M.Ohtsuka, J.Imai, L.F.Mase, T.Moriuchi, R.Tsuda, M.Nagata, K.Nagata, Y.Tanokura, M.

(2013) J Bacteriol 195: 2642-2651

  • DOI: 10.1128/JB.02020-12
  • Primary Citation of Related Structures:  
    4H77, 4H7K, 4H7D, 4H7E, 4H7F, 4H7H, 4H7I, 4H7J

  • PubMed Abstract: 
  • The enzymes LinB(UT) and LinB(MI) (LinB from Sphingobium japonicum UT26 and Sphingobium sp. MI1205, respectively) catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexano ...

    The enzymes LinB(UT) and LinB(MI) (LinB from Sphingobium japonicum UT26 and Sphingobium sp. MI1205, respectively) catalyze the hydrolytic dechlorination of β-hexachlorocyclohexane (β-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinB(MI) and its seven point mutants. The mutation analysis revealed that the seven amino acid residues uniquely found in LinB(MI) were categorized into three groups based on the efficiency of the first-step (from β-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. Crystal structure analyses of wild-type LinB(MI) and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinB(MI). The dynamics simulation analyses of wild-type LinB(MI) and LinB(UT) revealed that the entrance of the substrate access tunnel of LinB(UT) was more flexible than that of LinB(MI), which could lead to the different efficiencies of dehalogenation activity between these dehalogenases.


    Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenaseA302Sphingobium sp. MI1205Mutation(s): 1 
Gene Names: linBdhaAK663_22528K663_22543
EC: 3.8.1.5
Find proteins for A4PEU6 (Sphingobium sp. MI1205)
Explore A4PEU6 
Go to UniProtKB:  A4PEU6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.538α = 90
b = 72.153β = 90
c = 73.584γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release