2Y93

Crystal Structure of cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)from Pandoraea pnomenusa strain B-356.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical Studies and Ligand-Bound Structures of Biphenyl Dehydrogenase from Pandoraea Pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme.

Dhindwal, S.Patil, D.N.Mohammadi, M.Sylvestre, M.Tomar, S.Kumar, P.

(2011) J.Biol.Chem. 286: 37011

  • DOI: 10.1074/jbc.M111.291013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyzes the second step of the biphenyl/polychlorinated biphenyls catabolic pathway in bacteria. To understand the molecular basis for the broad substrate specificity ...

    Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyzes the second step of the biphenyl/polychlorinated biphenyls catabolic pathway in bacteria. To understand the molecular basis for the broad substrate specificity of Pandoraea pnomenusa strain B-356 biphenyl dehydrogenase (BphB(B-356)), the crystal structures of the apo-enzyme, the binary complex with NAD(+), and the ternary complexes with NAD(+)-2,3-dihydroxybiphenyl and NAD(+)-4,4'-dihydroxybiphenyl were determined at 2.2-, 2.5-, 2.4-, and 2.1-Å resolutions, respectively. A crystal structure representing an intermediate state of the enzyme was also obtained in which the substrate binding loop was ordered as compared with the apo and binary forms but it was displaced significantly with respect to the ternary structures. These five structures reveal that the substrate binding loop is highly mobile and that its conformation changes during ligand binding, starting from a disorganized loop in the apo state to a well organized loop structure in the ligand-bound form. Conformational changes are induced during ligand binding; forming a well defined cavity to accommodate a wide variety of substrates. This explains the biochemical data that shows BphB(B-356) converts the dihydrodiol metabolites of 3,3'-dichlorobiphenyl, 2,4,4'-trichlorobiphenyl, and 2,6-dichlorobiphenyl to their respective dihydroxy metabolites. For the first time, a combination of structural, biochemical, and molecular docking studies of BphB(B-356) elucidate the unique ability of the enzyme to transform the cis-dihydrodiols of double meta-, para-, and ortho-substituted chlorobiphenyls.


    Related Citations: 
    • Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Cis-Biphenyl-2,3-Dihydrodiol -2,3-Dehydrogenase from Pandoraea Pnomenusa B-356.
      Patil, D.N.,Tomar, S.,Sylvestre, M.,Kumar, P.
      (2010) Acta Crystallogr.,Sect.F 66: 1517


    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
A, B
281Comamonas testosteroniMutation(s): 0 
Gene Names: bphB
EC: 1.3.1.56
Find proteins for Q46381 (Comamonas testosteroni)
Go to UniProtKB:  Q46381
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 75.692α = 90.00
b = 75.692β = 90.00
c = 176.876γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references