Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 221.83 kDa 
• Atom Count: 15345 
• Residue Count: 1806 
• Unique protein chains: 2

1ULI

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

• DOI: 10.2210/pdb1ULI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Rhodococcus erythropolis
• Mutation(s): No 


• Deposited: 2003-09-12 Released: 2004-09-28 
• Deposition Author(s): Furusawa, Y., Nagarajan, V., Masai, E., Tanokura, M., Fukuda, M., Senda, T.

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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 

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

• PubMed: 15342255 
• 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 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.

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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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
biphenyl dioxygenase large subunit	A, C, E	460	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: bphA1, bphAa, RHA1_ro08060 EC: 1.14.12.18
Find proteins for Q53122 (Rhodococcus jostii (strain RHA1)) Explore Q53122  Go to UniProtKB:  Q53122

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
biphenyl dioxygenase small subunit	B, D, F	187	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: bphA2, bphAb, RHA1_ro08059 EC: 1.14.12.18
Find proteins for Q53123 (Rhodococcus jostii (strain RHA1)) Explore Q53123  Go to UniProtKB:  Q53123

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	A, C, E	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE2	A, B, C, E	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

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 = 137.741	α = 90
b = 137.741	β = 90
c = 237.744	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-12 
• Released Date: 2004-09-28 
Deposition Author(s): Furusawa, Y., Nagarajan, V., Masai, E., Tanokura, M., Fukuda, M., Senda, T.

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