1ULI

Biphenyl dioxygenase (BphA1A2) derived from Rhodococcus sp. strain RHA1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Terminal Oxygenase Component of Biphenyl Dioxygenase Derived from Rhodococcus sp. Strain RHA1

Furusawa, Y.Nagarajan, V.Tanokura, M.Masai, E.Fukuda, M.Senda, T.

(2004) J.Mol.Biol. 342: 1041-1052

  • DOI: 10.1016/j.jmb.2004.07.062
  • Primary Citation of Related Structures:  1ULJ

  • PubMed Abstract: 
  • Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious envir ...

    Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.


    Related Citations: 
    • Crystallization Of The Terminal Oxygenase Component Of Biphenyl Dioxygenase Derived From Rhodococcus Sp. Strain Rha1
      Nagarajan, V.,Sakurai, N.,Kubota, M.,Nonaka, T.,Nagumo, H.,Takeda, H.,Nishizaki, T.,Masai, E.,Fukuda, M.,Senda, T.
      (2003) Protein Pept.Lett. 10: 412


    Organizational Affiliation

    Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
biphenyl dioxygenase large subunit
A, C, E
460Rhodococcus jostii (strain RHA1)Gene Names: bphA1 (bphAa)
EC: 1.14.12.18
Find proteins for Q53122 (Rhodococcus jostii (strain RHA1))
Go to UniProtKB:  Q53122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
biphenyl dioxygenase small subunit
B, D, F
187Rhodococcus jostii (strain RHA1)Gene Names: bphA2 (bphAb)
EC: 1.14.12.18
Find proteins for Q53123 (Rhodococcus jostii (strain RHA1))
Go to UniProtKB:  Q53123
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
A, C, E
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, E
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 137.741α = 90.00
b = 137.741β = 90.00
c = 237.744γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance