3HPY

Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in the complex with 4-methylcatechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas

Cho, J.-H.Jung, D.-K.Lee, K.Rhee, S.

(2009) J.Biol.Chem. 284: 34321-34330

  • DOI: 10.1074/jbc.M109.031054
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LapB is a non-heme Fe(II)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in Pseudomonas sp. KL28 and belongs to the superfamily of type I extradiol dioxygenases. In this study, the cryst ...

    LapB is a non-heme Fe(II)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in Pseudomonas sp. KL28 and belongs to the superfamily of type I extradiol dioxygenases. In this study, the crystal structures of substrate-free LapB and its complexes with a substrate or product were determined, along with a functional analysis of the active site residues. Structural features of the homotetramer are similar to those of other type I extradiol dioxygenases. In particular, the active site is located in the C-domain of each monomer, with a 2-His-1-carboxylate motif as the first coordination shell to iron ion. A comparison of three different structures in the catalytic cycle indicated catalysis-related local conformational changes in the active site. Specifically, the active site loop containing His-248 exhibits positional changes upon binding of the substrate and establishes a hydrogen-bonding network with Tyr-257, which is near the hydroxyl group of the substrate. Kinetic analysis of the mutant enzymes H248A, H248N, and Y257F showed that these three mutant enzymes are inactive, suggesting that this hydrogen-bonding network plays a crucial role in catalysis by deprotonating the incoming substrate and leaving it in a monoanionic state. Additional functional analysis of His-201, by using H201A and H201N mutants, near the dioxygen-binding site also supports its role as base and acid catalyst in the late stage of catalysis. We also noticed a disordered-to-ordered structural transition in the C-terminal region, resulting in the opening or closing of the active site. These results provide detailed insights into the structural and functional features of an extradiol dioxygenase that can accommodate a wide range of alkylcatechols.


    Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catechol 2,3-dioxygenase
A, B, C, D
309Pseudomonas alkylphenolicaMutation(s): 0 
Gene Names: lapB
Find proteins for Q7WYF5 (Pseudomonas alkylphenolica)
Go to UniProtKB:  Q7WYF5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MCT
Query on MCT

Download SDF File 
Download CCD File 
A, B, C
4-METHYLCATECHOL
4-METHYL-1,2-BENZENEDIOL
C7 H8 O2
ZBCATMYQYDCTIZ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.100α = 90.00
b = 97.600β = 90.00
c = 133.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
DENZOdata reduction
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-06-05 
  • Released Date: 2009-10-20 
  • Deposition Author(s): Cho, J.-H., Rhee, S.

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references
  • Version 1.3: 2017-11-01
    Type: Refinement description