1EIR

2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • Primary Citation of Related Structures:  1EIL, 1EIM, 1EIQ

  • 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 ...

    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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-DIHYDROXYBIPHENYL-1,2-DIOXYGENASE
A
292Pseudomonas sp. (strain KKS102)Gene Names: bphC
EC: 1.13.11.39
Find proteins for P17297 (Pseudomonas sp. (strain KKS102))
Go to UniProtKB:  P17297
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BPY
Query on BPY

Download SDF File 
Download CCD File 
A
BIPHENYL-2,3-DIOL
C12 H10 O2
YKOQAAJBYBTSBS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.600α = 90.00
b = 121.600β = 90.00
c = 108.700γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-02-28 
  • Released Date: 2001-02-28 
  • Deposition Author(s): Senda, T.

Revision History 

  • Version 1.0: 2001-02-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description