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

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1371/journal.pone.0052550
  • Primary Citation of Related Structures:  3GZX

  • 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 dioxyge ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Biphenyl dioxygenase subunit alpha
A
457Comamonas testosteroniGene Names: bphA
EC: 1.14.12.18
Find proteins for Q46372 (Comamonas testosteroni)
Go to UniProtKB:  Q46372
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Biphenyl dioxygenase subunit beta
B
186Comamonas testosteroniGene Names: bphE
EC: 1.14.12.18
Find proteins for Q46373 (Comamonas testosteroni)
Go to UniProtKB:  Q46373
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

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

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
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 = 90.00
b = 136.233β = 90.00
c = 106.237γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXL-97refinement
SHELXmodel building
SCALEPACKdata scaling
SHELXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-02-06
    Type: Database references