1ULI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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, 1ULI

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
biphenyl dioxygenase large subunitACE460Rhodococcus jostii RHA1Mutation(s): 0 
Gene Names: bphA1bphAaRHA1_ro08060
EC: 1.14.12.18
Find proteins for Q53122 (Rhodococcus jostii (strain RHA1))
Explore Q53122 
Go to UniProtKB:  Q53122
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
biphenyl dioxygenase small subunitBDF187Rhodococcus jostii RHA1Mutation(s): 0 
Gene Names: bphA2bphAbRHA1_ro08059
EC: 1.14.12.18
Find proteins for Q53123 (Rhodococcus jostii (strain RHA1))
Explore Q53123 
Go to UniProtKB:  Q53123
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.741α = 90
b = 137.741β = 90
c = 237.744γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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