3GZY

Crystal Structure of the Biphenyl Dioxygenase from Comamonas testosteroni Sp. Strain B-356


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes

Colbert, C.L.Agar, N.Y.Kumar, P.Chakko, M.N.Sinha, S.C.Powlowski, J.B.Eltis, L.D.Bolin, J.T.

(2013) PLoS One 8: e52550-e52550

  • DOI: https://doi.org/10.1371/journal.pone.0052550
  • Primary Citation of Related Structures:  
    3GZX, 3GZY

  • PubMed Abstract: 

    The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a heterohexameric (αβ)(3) Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356) with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDO(B356) and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA. christopher.colbert@ndsu.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Biphenyl dioxygenase subunit alpha457Comamonas testosteroniMutation(s): 0 
Gene Names: bphA
EC: 1.14.12.18
UniProt
Find proteins for Q46372 (Comamonas testosteroni)
Explore Q46372 
Go to UniProtKB:  Q46372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46372
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Biphenyl dioxygenase subunit beta186Comamonas testosteroniMutation(s): 0 
Gene Names: bphE
EC: 1.14.12.18
UniProt
Find proteins for Q46373 (Comamonas testosteroni)
Explore Q46373 
Go to UniProtKB:  Q46373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46373
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.233α = 90
b = 136.233β = 90
c = 106.237γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-02-06
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description