1EIL

2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.

Uragami, Y.Senda, T.Sugimoto, K.Sato, N.Nagarajan, V.Masai, E.Fukuda, M.Mitsu, Y.

(2001) J Inorg Biochem 83: 269-279

  • DOI: 10.1016/s0162-0134(00)00172-0
  • Primary Citation of Related Structures:  
    1EIL, 1EIQ, 1EIR

  • PubMed Abstract: 
  • BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site ...

    BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.


    Related Citations: 
    • Three-dimensional Structure of 2,3-dihydroxybiphenyl dioxygenase (BphC enzyme) from Pseudomonas sp. strain KKS102 having Polychlorinated Biphenyl (PCB) Degrading Activity.
      Sugiyama, K., Senda, T., Kimbara, K., Fukuda, M., Mitsui, Y.
      (1995) Proc Jpn Acad Ser B Phys Biol Sci 71: 32
    • Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102.
      Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., Sato, M., Yano, K., Mitsui, Y.
      (1996) J Mol Biol 255: 735

    Organizational Affiliation

    Department of BioEngineering, Nagaoka University of Technology, Niigata, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASEA292Pseudomonas sp. KKS102Mutation(s): 0 
Gene Names: bphC
EC: 1.13.11.39
UniProt
Find proteins for P17297 (Pseudomonas sp. (strain KKS102))
Explore P17297 
Go to UniProtKB:  P17297
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.75α = 90
b = 121.75β = 90
c = 108.86γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2000-02-26 
  • Released Date: 2001-02-26 
  • Deposition Author(s): Senda, T.

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance